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- PDB-4yuu: Crystal structure of oxygen-evolving photosystem II from a red alga -

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Basic information

Entry
Database: PDB / ID: 4yuu
TitleCrystal structure of oxygen-evolving photosystem II from a red alga
Components
  • (Cytochrome b559 subunit ...) x 2
  • (PEPTIDE CHAIN ...) x 2
  • (PHOTOSYSTEM II REACTION CENTER PROTEIN ...) x 10
  • (Photosystem II ...) x 6
  • Cytochrome c-550
  • Extrinsic protein in photosystem IIPeripheral membrane protein
KeywordsPHOTOSYNTHESIS / TRANSMEMBRANE ALPHA-HELIX / ELECTRON TRANSPORT / PHOTOSYSTEM II / WATER-SPLITTING / OXYGEN-EVOLVING / IRON BINDING / CALCIUM BINDING / MANGANESE BINDING / CHLORIDE BINDING / THYLAKOID MEMBRANE
Function / homology
Function and homology information


photosystem II reaction center / photosystem II / photosystem II stabilization / photosystem II oxygen evolving complex / cytochrome c-heme linkage / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem II / photosynthetic electron transport chain / chlorophyll binding / photosynthetic electron transport in photosystem II ...photosystem II reaction center / photosystem II / photosystem II stabilization / photosystem II oxygen evolving complex / cytochrome c-heme linkage / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem II / photosynthetic electron transport chain / chlorophyll binding / photosynthetic electron transport in photosystem II / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / response to herbicide / respiratory electron transport chain / photosynthesis / extrinsic component of membrane / protein-chromophore linkage / protein stabilization / oxidation-reduction process / electron transfer activity / iron ion binding / calcium ion binding / heme binding / integral component of membrane / metal ion binding
Photosystem II complex subunit Ycf12 / Photosystem II PsbV, cytochrome c-550 precursor / Cytochrome c-like domain superfamily / Photosystem II reaction centre protein H superfamily / Photosystem II protein D1/D2 superfamily / Photosystem antenna protein-like superfamily / Cytochrome c-550 domain / PsbQ-like domain superfamily / Photosystem II CP47 reaction centre protein / Photosystem II PsbL superfamily ...Photosystem II complex subunit Ycf12 / Photosystem II PsbV, cytochrome c-550 precursor / Cytochrome c-like domain superfamily / Photosystem II reaction centre protein H superfamily / Photosystem II protein D1/D2 superfamily / Photosystem antenna protein-like superfamily / Cytochrome c-550 domain / PsbQ-like domain superfamily / Photosystem II CP47 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II cytochrome c-550 precursor / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II PsbU, oxygen evolving complex / Photosystem II reaction centre protein Ycf12 / Cytochrome c-like domain / Oxygen-evolving enhancer protein 3 / Twin-arginine translocation pathway, signal sequence / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II PsbJ superfamily / Photosystem II cytochrome b559, alpha subunit / PsbJ / Cytochrome c-550 domain / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II reaction centre T protein / Oxygen evolving enhancer protein 3 (PsbQ) / PsbL protein / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II PsbT superfamily / Photosystem II 10 kDa phosphoprotein / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Photosystem II protein / Photosynthetic reaction centre protein / Photosystem II PsbI superfamily / Photosystem II PsbK superfamily / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, conserved site / Photosystem II CP43 reaction centre protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II PsbK / Photosystem II PsbI / Photosystem II PsbL / Photosystem II PsbJ / Photosystem II PsbT / Photosystem II reaction centre protein H / Photosystem antenna protein-like / Photosynthetic reaction centre, L/M
Cytochrome b559 subunit alpha / Photosystem II 12 kDa extrinsic protein, chloroplastic / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein K / Cytochrome c-550 ...Cytochrome b559 subunit alpha / Photosystem II 12 kDa extrinsic protein, chloroplastic / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein J / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein Ycf12 / Photosystem II reaction center protein K / Cytochrome c-550 / Extrinsic protein in photosystem II / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II protein D1 / Photosystem II reaction center protein I / Photosystem II reaction center protein H
Biological speciesCyanidium caldarium (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.77000368116 Å
AuthorsAgo, H. / Shen, J.-R.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS24000018 Japan
Citation
Journal: J.Biol.Chem. / Year: 2016
Title: Novel Features of Eukaryotic Photosystem II Revealed by Its Crystal Structure Analysis from a Red Alga
Authors: Ago, H. / Adachi, H. / Umena, Y. / Tashiro, T. / Kawakami, K. / Kamiya, N. / Tian, L. / Han, G. / Kuang, T. / Liu, Z. / Wang, F. / Zou, H. / Enami, I. / Miyano, M. / Shen, J.-R.
#1: Journal: Biochim. Biophys. Acta / Year: 2009
Title: Towards structural elucidation of eukaryotic photosystem II: Purification, crystallization and preliminary X-ray diffraction analysis of photosystem II from a red alga.
Authors: Adachi, H. / Umena, Y. / Enami, I. / Henmi, T. / Kamiya, N. / Shen, J.-R.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 23, 2016Group: Database references
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Derived calculations
Category: atom_type / citation ...atom_type / citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A1: Photosystem II protein D1
B1: Photosystem II CP47 reaction center protein
C1: Photosystem II CP43 reaction center protein
D1: Photosystem II D2 protein
E1: Cytochrome b559 subunit alpha
F1: Cytochrome b559 subunit beta
H1: Photosystem II reaction center protein H
I1: Photosystem II reaction center protein I
J1: Photosystem II reaction center protein J
K1: Photosystem II reaction center protein K
L1: Photosystem II reaction center protein L
M1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T1: Photosystem II reaction center protein T
U1: Photosystem II 12 kDa extrinsic protein, chloroplastic
V1: Cytochrome c-550
Y1: Photosystem II reaction center protein Ycf12
X1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S1: PEPTIDE CHAIN UNASSIGNED
W1: PEPTIDE CHAIN UNASSIGNED
a1: Photosystem II protein D1
b1: Photosystem II CP47 reaction center protein
c1: Photosystem II CP43 reaction center protein
d1: Photosystem II D2 protein
e1: Cytochrome b559 subunit alpha
f1: Cytochrome b559 subunit beta
h1: Photosystem II reaction center protein H
i1: Photosystem II reaction center protein I
j1: Photosystem II reaction center protein J
k1: Photosystem II reaction center protein K
l1: Photosystem II reaction center protein L
m1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t1: Photosystem II reaction center protein T
u1: Photosystem II 12 kDa extrinsic protein, chloroplastic
v1: Cytochrome c-550
y1: Photosystem II reaction center protein Ycf12
x1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s1: PEPTIDE CHAIN UNASSIGNED
w1: PEPTIDE CHAIN UNASSIGNED
q1: Extrinsic protein in photosystem II
A2: Photosystem II protein D1
B2: Photosystem II CP47 reaction center protein
C2: Photosystem II CP43 reaction center protein
D2: Photosystem II D2 protein
E2: Cytochrome b559 subunit alpha
F2: Cytochrome b559 subunit beta
H2: Photosystem II reaction center protein H
I2: Photosystem II reaction center protein I
J2: Photosystem II reaction center protein J
K2: Photosystem II reaction center protein K
L2: Photosystem II reaction center protein L
M2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T2: Photosystem II reaction center protein T
U2: Photosystem II 12 kDa extrinsic protein, chloroplastic
V2: Cytochrome c-550
Y2: Photosystem II reaction center protein Ycf12
X2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S2: PEPTIDE CHAIN UNASSIGNED
W2: PEPTIDE CHAIN UNASSIGNED
Q2: Extrinsic protein in photosystem II
Z2: Photosystem II reaction center protein Z
a2: Photosystem II protein D1
b2: Photosystem II CP47 reaction center protein
c2: Photosystem II CP43 reaction center protein
d2: Photosystem II D2 protein
e2: Cytochrome b559 subunit alpha
f2: Cytochrome b559 subunit beta
h2: Photosystem II reaction center protein H
i2: Photosystem II reaction center protein I
j2: Photosystem II reaction center protein J
k2: Photosystem II reaction center protein K
l2: Photosystem II reaction center protein L
m2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t2: Photosystem II reaction center protein T
u2: Photosystem II 12 kDa extrinsic protein, chloroplastic
v2: Cytochrome c-550
y2: Photosystem II reaction center protein Ycf12
x2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s2: PEPTIDE CHAIN UNASSIGNED
w2: PEPTIDE CHAIN UNASSIGNED
z2: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,579,524437
Polymers1,359,22484
Non-polymers220,300353
Water32418
1
A1: Photosystem II protein D1
B1: Photosystem II CP47 reaction center protein
C1: Photosystem II CP43 reaction center protein
D1: Photosystem II D2 protein
E1: Cytochrome b559 subunit alpha
F1: Cytochrome b559 subunit beta
H1: Photosystem II reaction center protein H
I1: Photosystem II reaction center protein I
J1: Photosystem II reaction center protein J
K1: Photosystem II reaction center protein K
L1: Photosystem II reaction center protein L
M1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T1: Photosystem II reaction center protein T
U1: Photosystem II 12 kDa extrinsic protein, chloroplastic
V1: Cytochrome c-550
Y1: Photosystem II reaction center protein Ycf12
X1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S1: PEPTIDE CHAIN UNASSIGNED
W1: PEPTIDE CHAIN UNASSIGNED
hetero molecules


Theoretical massNumber of molelcules
Total (without water)381,162103
Polymers324,53220
Non-polymers56,62983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
a1: Photosystem II protein D1
b1: Photosystem II CP47 reaction center protein
c1: Photosystem II CP43 reaction center protein
d1: Photosystem II D2 protein
e1: Cytochrome b559 subunit alpha
f1: Cytochrome b559 subunit beta
h1: Photosystem II reaction center protein H
i1: Photosystem II reaction center protein I
j1: Photosystem II reaction center protein J
k1: Photosystem II reaction center protein K
l1: Photosystem II reaction center protein L
m1: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o1: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t1: Photosystem II reaction center protein T
u1: Photosystem II 12 kDa extrinsic protein, chloroplastic
v1: Cytochrome c-550
y1: Photosystem II reaction center protein Ycf12
x1: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s1: PEPTIDE CHAIN UNASSIGNED
w1: PEPTIDE CHAIN UNASSIGNED
q1: Extrinsic protein in photosystem II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,739112
Polymers348,59621
Non-polymers55,14391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A2: Photosystem II protein D1
B2: Photosystem II CP47 reaction center protein
C2: Photosystem II CP43 reaction center protein
D2: Photosystem II D2 protein
E2: Cytochrome b559 subunit alpha
F2: Cytochrome b559 subunit beta
H2: Photosystem II reaction center protein H
I2: Photosystem II reaction center protein I
J2: Photosystem II reaction center protein J
K2: Photosystem II reaction center protein K
L2: Photosystem II reaction center protein L
M2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
O2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
T2: Photosystem II reaction center protein T
U2: Photosystem II 12 kDa extrinsic protein, chloroplastic
V2: Cytochrome c-550
Y2: Photosystem II reaction center protein Ycf12
X2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
S2: PEPTIDE CHAIN UNASSIGNED
W2: PEPTIDE CHAIN UNASSIGNED
Q2: Extrinsic protein in photosystem II
Z2: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)407,319108
Polymers355,08022
Non-polymers52,23986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
a2: Photosystem II protein D1
b2: Photosystem II CP47 reaction center protein
c2: Photosystem II CP43 reaction center protein
d2: Photosystem II D2 protein
e2: Cytochrome b559 subunit alpha
f2: Cytochrome b559 subunit beta
h2: Photosystem II reaction center protein H
i2: Photosystem II reaction center protein I
j2: Photosystem II reaction center protein J
k2: Photosystem II reaction center protein K
l2: Photosystem II reaction center protein L
m2: PHOTOSYSTEM II REACTION CENTER PROTEIN M
o2: PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO
t2: Photosystem II reaction center protein T
u2: Photosystem II 12 kDa extrinsic protein, chloroplastic
v2: Cytochrome c-550
y2: Photosystem II reaction center protein Ycf12
x2: PHOTOSYSTEM II REACTION CENTER PROTEIN X
s2: PEPTIDE CHAIN UNASSIGNED
w2: PEPTIDE CHAIN UNASSIGNED
z2: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)387,305114
Polymers331,01621
Non-polymers56,28893
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)210.445, 240.31, 300.063
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
21chain A2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
31chain a1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
41chain a2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
12chain B1 and (resseq 2:481)
22chain B2 and (resseq 2:481)
32chain b1 and (resseq 2:481)
42chain b2 and (resseq 2:481)
13chain C1 and (resseq 26:146 or resseq 155:472)
23chain C2 and (resseq 26:146 or resseq 155:472)
33chain c1 and (resseq 26:146 or resseq 155:472)
43chain c2 and (resseq 26:146 or resseq 155:472)
14chain D1 and (resseq 14:235 or resseq 239:352)
24chain D2 and (resseq 14:235 or resseq 239:352)
34chain d1 and (resseq 14:235 or resseq 239:352)
44chain d2 and (resseq 14:235 or resseq 239:352)
15chain E1 and (resseq 23:78 )
25chain E2 and (resseq 23:78)
35chain e1 and (resseq 23:78 )
45chain e2 and (resseq 23:78)
16chain F1 and (resseq 18:44 )
26chain F2 and (resseq 18:44)
36chain f1 and (resseq 18:44 )
46chain f2 and (resseq 18:44)
17chain H1 and (resseq 2:55 or resseq 58:63)
27chain H2 and (resseq 2:55 or resseq 58:63)
37chain h1 and (resseq 2:55 or resseq 58:63)
47chain h2 and (resseq 2:55 or resseq 58:63)
18chain I1 and (resseq 1:32)
28chain I2 and (resseq 1:32)
38chain i1 and (resseq 1:32)
48chain i2 and (resseq 1:32)
19chain J1 and (resseq 9:39)
29chain J2 and (resseq 9:39)
39chain j1 and (resseq 9:39)
49chain j2 and (resseq 9:39)
110chain K1 and (resseq 10:44)
210chain K2 and (resseq 10:44)
310chain k1 and (resseq 10:44)
410chain k2 and (resseq 10:44)
111chain L1 and (resseq 2:38)
211chain L2 and (resseq 2:38)
311chain l1 and (resseq 2:38)
411chain l2 and (resseq 2:38)
112chain M1 and (resseq 1:40 )
212chain M2 and (resseq 1:40)
312chain m1 and (resseq 1:40 )
412chain m2 and (resseq 1:40)
113chain O1 and (resseq -2:22 or resseq 39:54 or resseq...
213chain O2 and (resseq -2:22 or resseq 39:54 or resseq...
313chain o1 and (resseq -2:22 or resseq 39:54 or resseq...
413chain o2 and (resseq -2:22 or resseq 39:54 or resseq...
114chain T1 and (resseq 1:29)
214chain T2 and (resseq 1:29)
314chain t1 and (resseq 1:29)
414chain t2 and (resseq 1:29)
115chain U1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
215chain U2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
315chain u1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
415chain u2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
116chain V1 and (resseq 9:137)
216chain V2 and (resseq 9:137)
316chain v1 and (resseq 9:137)
416chain v2 and (resseq 9:137)
117chain Y1 and (resseq 16:40)
217chain Y2 and (resseq 16:40)
317chain y1 and (resseq 16:40)
417chain y2 and (resseq 16:40)
118chain X1 and (resseq 5:31)
218chain X2 and (resseq 5:31)
318chain x1 and (resseq 5:31)
418chain x2 and (resseq 5:31)
119chain S1 and (resseq 8:31)
219chain S2 and (resseq 8:31)
319chain s1 and (resseq 8:31)
419chain s2 and (resseq 8:31)
120chain W1 and (resseq 4:21)
220chain W2 and (resseq 4:21)
320chain w1 and (resseq 4:21)
420chain w2 and (resseq 4:21)
121chain q1 and (resseq 109:217)
221chain Q2 and (resseq 109:217 )
122chain Z2 and (resseq 2:58)
222chain z2 and (resseq 2:58)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
211chain A2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
311chain a1 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
411chain a2 and (resseq 11:303 or resseq 305:314 or resseq 316:344)
112chain B1 and (resseq 2:481)
212chain B2 and (resseq 2:481)
312chain b1 and (resseq 2:481)
412chain b2 and (resseq 2:481)
113chain C1 and (resseq 26:146 or resseq 155:472)
213chain C2 and (resseq 26:146 or resseq 155:472)
313chain c1 and (resseq 26:146 or resseq 155:472)
413chain c2 and (resseq 26:146 or resseq 155:472)
114chain D1 and (resseq 14:235 or resseq 239:352)
214chain D2 and (resseq 14:235 or resseq 239:352)
314chain d1 and (resseq 14:235 or resseq 239:352)
414chain d2 and (resseq 14:235 or resseq 239:352)
115chain E1 and (resseq 23:78 )
215chain E2 and (resseq 23:78)
315chain e1 and (resseq 23:78 )
415chain e2 and (resseq 23:78)
116chain F1 and (resseq 18:44 )
216chain F2 and (resseq 18:44)
316chain f1 and (resseq 18:44 )
416chain f2 and (resseq 18:44)
117chain H1 and (resseq 2:55 or resseq 58:63)
217chain H2 and (resseq 2:55 or resseq 58:63)
317chain h1 and (resseq 2:55 or resseq 58:63)
417chain h2 and (resseq 2:55 or resseq 58:63)
118chain I1 and (resseq 1:32)
218chain I2 and (resseq 1:32)
318chain i1 and (resseq 1:32)
418chain i2 and (resseq 1:32)
119chain J1 and (resseq 9:39)
219chain J2 and (resseq 9:39)
319chain j1 and (resseq 9:39)
419chain j2 and (resseq 9:39)
1110chain K1 and (resseq 10:44)
2110chain K2 and (resseq 10:44)
3110chain k1 and (resseq 10:44)
4110chain k2 and (resseq 10:44)
1111chain L1 and (resseq 2:38)
2111chain L2 and (resseq 2:38)
3111chain l1 and (resseq 2:38)
4111chain l2 and (resseq 2:38)
1112chain M1 and (resseq 1:40 )
2112chain M2 and (resseq 1:40)
3112chain m1 and (resseq 1:40 )
4112chain m2 and (resseq 1:40)
1113chain O1 and (resseq -2:22 or resseq 39:54 or resseq...
2113chain O2 and (resseq -2:22 or resseq 39:54 or resseq...
3113chain o1 and (resseq -2:22 or resseq 39:54 or resseq...
4113chain o2 and (resseq -2:22 or resseq 39:54 or resseq...
1114chain T1 and (resseq 1:29)
2114chain T2 and (resseq 1:29)
3114chain t1 and (resseq 1:29)
4114chain t2 and (resseq 1:29)
1115chain U1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
2115chain U2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
3115chain u1 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
4115chain u2 and (resseq 11:68 or resseq 73:93 or resseq 96:103)
1116chain V1 and (resseq 9:137)
2116chain V2 and (resseq 9:137)
3116chain v1 and (resseq 9:137)
4116chain v2 and (resseq 9:137)
1117chain Y1 and (resseq 16:40)
2117chain Y2 and (resseq 16:40)
3117chain y1 and (resseq 16:40)
4117chain y2 and (resseq 16:40)
1118chain X1 and (resseq 5:31)
2118chain X2 and (resseq 5:31)
3118chain x1 and (resseq 5:31)
4118chain x2 and (resseq 5:31)
1119chain S1 and (resseq 8:31)
2119chain S2 and (resseq 8:31)
3119chain s1 and (resseq 8:31)
4119chain s2 and (resseq 8:31)
1120chain W1 and (resseq 4:21)
2120chain W2 and (resseq 4:21)
3120chain w1 and (resseq 4:21)
4120chain w2 and (resseq 4:21)
1121chain q1 and (resseq 109:217)
2121chain Q2 and (resseq 109:217 )
1122chain Z2 and (resseq 2:58)
2122chain z2 and (resseq 2:58)

NCS ensembles:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22

NCS oper:
IDCodeMatrixVector
1given(-0.994688217729, -0.101094938656, -0.0193691220559), (-0.0866947037877, 0.924242778818, -0.371832373708), (0.0554921422026, -0.368178080799, -0.928097798173)433.120859872, 47.0809240207, 135.025280081
2given(-0.0861082173904, -0.144006686415, -0.985823234239), (-0.148360252587, -0.976612344918, 0.155619931908), (-0.985177451199, 0.159657138965, 0.0627294797315)297.039492026, 285.997598022, 233.44479834
3given(0.0462949424116, 0.214399564113, 0.97564829996), (0.242276162477, -0.949943576186, 0.197254817832), (0.969102182127, 0.22724442561, -0.0959214867839)122.244648675, 197.87423474, -177.849810215
4given(-0.99511539619, -0.0960614193251, -0.0227497688494), (-0.0811593959149, 0.927289004356, -0.365442546585), (0.0562005402124, -0.361811147033, -0.930555851716)432.495343171, 45.3075450849, 134.186589846
5given(-0.0888791646716, -0.147684105777, -0.985032943098), (-0.148228629518, -0.97597338248, 0.159700438577), (-0.984951149793, 0.160204124764, 0.0648526863757)297.862583106, 285.625213502, 233.188675125
6given(0.045584286663, 0.216906868873, 0.975127418877), (0.24733465169, -0.948199958182, 0.199354983326), (0.967857243029, 0.232095345794, -0.0968716035696)122.187176474, 196.225389507, -178.189790032
7given(-0.994875114783, -0.0993255838258, -0.018919153888), (-0.0852498218619, 0.924605162241, -0.371265082966), (0.0543688684698, -0.367749537532, -0.928334155241)433.030837872, 46.9130273562, 135.259178975
8given(-0.0817664181085, -0.142766251961, -0.986373179973), (-0.145738949628, -0.977336076679, 0.153539414431), (-0.985938340583, 0.156307359147, 0.0591066666752)296.202587607, 285.874408822, 234.306620338
9given(0.0464773443275, 0.214611694311, 0.975592987433), (0.239868898215, -0.950470557124, 0.197657865284), (0.969692099655, 0.224827802338, -0.0956540180152)122.118997349, 198.648341474, -177.617850767
10given(-0.994994824437, -0.0978284927247, -0.0203687347392), (-0.0834360691764, 0.925521998083, -0.369387944342), (0.0549883779, -0.365839605669, -0.929052022881)432.798429673, 46.139573157, 134.910835703
11given(-0.0877814784142, -0.148367745888, -0.985028641222), (-0.147165050057, -0.976063600916, 0.160132117357), (-0.985209043853, 0.159018423296, 0.0638457591642)297.874736427, 285.415512164, 233.481810323
12given(0.0461342899598, 0.21279757064, 0.976006568226), (0.241248555903, -0.950499161352, 0.195832782097), (0.969366164855, 0.226425568783, -0.0951877105329)122.520826276, 198.256492365, -177.86500981
13given(-0.993681686101, -0.112233964083, -0.00049397814865), (-0.104658516429, 0.928182955191, -0.3571036217), (0.0405376571497, -0.354795629904, -0.934064644098)434.969452945, 50.6076417004, 136.310811595
14given(-0.102256877186, -0.165513387095, -0.980891864458), (-0.15822989713, -0.970800238959, 0.180305839318), (-0.982093086587, 0.173643930876, 0.0730818345933)301.68807023, 284.856006245, 230.838305638
15given(0.0421528222667, 0.20891687859, 0.977024501952), (0.250522432498, -0.94886313853, 0.19208658244), (0.967192664566, 0.23666956327, -0.0923356238483)124.048082421, 195.441331685, -178.650382784
16given(-0.991360751479, -0.130609618425, 0.0120410964108), (-0.124861245463, 0.911627605193, -0.391592618458), (0.0401687665898, -0.389713018803, -0.920059907379)436.722037925, 55.4545239229, 140.884214806
17given(-0.108002962146, -0.186115690701, -0.976573760575), (-0.165566197286, -0.96523398559, 0.202265141281), (-0.980266899617, 0.183532838305, 0.0734336624435)304.990091218, 284.467860872, 229.27244508
18given(0.0411398303761, 0.209516604269, 0.976939254454), (0.249195632692, -0.949020010334, 0.193035117618), (0.967578963705, 0.235507563619, -0.0912531450089)124.248869462, 195.948436818, -178.699766945
19given(-0.994791522452, -0.098850470402, -0.0248678780692), (-0.0831338961891, 0.927995980253, -0.363197213561), (0.0589795062949, -0.359238145435, -0.931380358769)432.902663296, 45.5133040734, 133.102652489
20given(-0.0900195954688, -0.148778699132, -0.984764627267), (-0.147272410351, -0.975920292574, 0.16090500207), (-0.984991020051, 0.159513263481, 0.0659409523174)298.163301597, 285.256515643, 233.256195273
21given(0.0443246621877, 0.213692675301, 0.975894853375), (0.240249008663, -0.950467019249, 0.197212725647), (0.969698787335, 0.225716383639, -0.0934685829484)122.807138076, 198.33388471, -178.13203079
22given(-0.994981896228, -0.0977002039087, -0.0215799985024), (-0.0832816903506, 0.928227787117, -0.362570455603), (0.0554543616995, -0.358953820679, -0.931706481886)433.092716715, 45.777667289, 134.198513206
23given(-0.0826279580462, -0.143439491014, -0.986203697502), (-0.150067860639, -0.97651291149, 0.154603269357), (-0.985216858236, 0.160772031492, 0.0591616103346)296.556716825, 286.347046123, 233.415933203
24given(0.0495438851498, 0.216384330723, 0.975050370423), (0.239312541956, -0.950382997007, 0.198750261036), (0.969677735491, 0.223494922575, -0.098869150277)121.234571824, 198.589537337, -177.279204537
25given(-0.996380597315, -0.0835178726258, -0.0158262517877), (-0.0721871763766, 0.929662753884, -0.361270225188), (0.0448855974713, -0.358820190336, -0.932326849419)431.628589293, 43.932309601, 136.142401096
26given(-0.0857481117677, -0.131034577298, -0.987662493406), (-0.148716049158, -0.978524724117, 0.14273367162), (-0.985155215208, 0.159120406748, 0.0644197027723)295.274730598, 286.725286328, 233.548367416
27given(0.0539346215476, 0.223494077448, 0.973211926532), (0.240811562435, -0.94877527477, 0.204536718909), (0.969072158302, 0.223329074082, -0.104991793364)118.682982232, 197.647325619, -176.64229757
28given(-0.994276018151, -0.105466634091, -0.0170876804323), (-0.0911840323755, 0.920994052803, -0.378755101538), (0.0556836777582, -0.375028990606, -0.925339172539)433.449280555, 48.1633132464, 135.688387074
29given(-0.0813506823574, -0.134166402877, -0.987614015098), (-0.144834436866, -0.978788870649, 0.144897662479), (-0.986106004635, 0.154828043432, 0.060193227104)294.802043198, 286.234374787, 234.503956686
30given(0.0539170868628, 0.214846838969, 0.975158337671), (0.238193368702, -0.951154806022, 0.196388528401), (0.969719994045, 0.221687552123, -0.102458588625)120.030461539, 199.39782297, -176.753479995
31given(-0.994210362084, -0.105884307838, -0.0182830325316), (-0.0916584392649, 0.924515913332, -0.369958182107), (0.0560757205609, -0.366140463962, -0.928868491345)433.556686803, 48.0705136935, 134.718529303
32given(-0.0894508324748, -0.140278570416, -0.986063117276), (-0.155149910898, -0.975983735371, 0.152919107503), (-0.9838328383, 0.166666346252, 0.06553834991)297.126293269, 287.299091056, 232.007532403
33given(0.048299628765, 0.218078798676, 0.974735237605), (0.248710833272, -0.947763017532, 0.199720264401), (0.967372765419, 0.232780798537, -0.100015161642)121.369115974, 195.890494843, -178.117128846
34given(-0.994375388868, -0.104984960034, -0.013990860598), (-0.0921494394209, 0.922692129294, -0.374363079581), (0.0522117499038, -0.370968182875, -0.927176650087)433.39872118, 48.5326708682, 136.124614248
35given(-0.0863855400729, -0.142455513077, -0.986024322854), (-0.15951766953, -0.974977075417, 0.154834800736), (-0.983408181568, 0.170663789965, 0.0614997497609)296.975578231, 287.855453757, 231.604085779
36given(0.0477869785461, 0.217062277331, 0.974987370401), (0.241980675524, -0.94954213054, 0.199537202053), (0.96910358443, 0.226392822523, -0.09790062592)121.695641982, 197.764921612, -177.793529402
37given(-0.995440236131, -0.0950926451487, -0.00749167069322), (-0.0854738869113, 0.924095165172, -0.372481328877), (0.0423432514981, -0.370142559758, -0.928009447424)432.784805281, 46.9933101494, 138.384813685
38given(-0.0765342294589, -0.150759479856, -0.985603414642), (-0.145261140303, -0.976269990424, 0.160611664942), (-0.98642876724, 0.155462165916, 0.0528185775056)296.630410407, 285.2439603, 235.03988298
39given(0.0373162324461, 0.208790064724, 0.977248283533), (0.244012480677, -0.950230595268, 0.193700090581), (0.969053872636, 0.231232620297, -0.0864064074045)125.456935812, 197.493272556, -178.538510571
40given(-0.995674515425, -0.0916542963121, -0.01522331437), (-0.0801978707902, 0.930557396903, -0.357255136548), (0.0469101359365, -0.354488957566, -0.93388276465)432.192364995, 44.4968786355, 135.527192025
41given(-0.0840541298632, -0.154111145098, -0.98447176608), (-0.139562310623, -0.976409192332, 0.164764834183), (-0.98663937926, 0.151244319186, 0.0605631175492)298.082289788, 283.790209629, 235.077925276
42given(0.0477002972203, 0.217226598394, 0.974955017729), (0.239320578279, -0.950121978493, 0.199984716409), (0.969768190063, 0.223787468227, -0.0973078959149)121.659267462, 198.462178265, -177.51018097
43given(-0.994134811123, -0.107558599792, -0.0112749688866), (-0.0960028049691, 0.925684862313, -0.365911187481), (0.0497939629952, -0.362682620615, -0.930581473033)433.796814147, 49.4673391561, 135.723051226
44given(-0.0890135934054, -0.152265767032, -0.984322973611), (-0.14709900338, -0.975399542379, 0.164187745987), (-0.985108351093, 0.159407869686, 0.0644256756937)298.503388512, 285.068197966, 233.305204242
45given(0.0443419800112, 0.208652275693, 0.976984143503), (0.241717982365, -0.95112934946, 0.192159771015), (0.969332866362, 0.227633891245, -0.0926099656984)123.513216997, 198.390792481, -178.053081209
46given(-0.994742426285, -0.101344504743, -0.0147240180324), (-0.0884760221118, 0.922882843507, -0.374778935737), (0.0515703292601, -0.37150578531, -0.926997277569)433.259447053, 47.6889621078, 136.280110871
47given(-0.0875251571543, -0.155302054795, -0.983982021503), (-0.143637632111, -0.975482924588, 0.166737201843), (-0.985752290135, 0.155930547403, 0.0630720768632)298.828683184, 284.47104027, 234.214095945
48given(0.0386178150388, 0.212533884124, 0.976390297197), (0.235092504672, -0.951624389873, 0.197844724081), (0.97120552851, 0.221901709544, -0.0867147778208)124.727899869, 200.31521905, -177.824386223
49given(-0.994447848264, -0.100574626792, -0.0309551535121), (-0.080992031864, 0.919334180335, -0.385051886949), (0.0671845805066, -0.380406899667, -0.922375640847)432.605478233, 46.2883935595, 134.595329682
50given(-0.0841938014331, -0.142847306695, -0.986157214023), (-0.138149049552, -0.978440191924, 0.153524040256), (-0.986826349419, 0.149162454387, 0.062644379582)296.29325265, 285.083441673, 235.541140406
51given(0.0545452606973, 0.181299452687, 0.98191411182), (0.224907504635, -0.96033861858, 0.164822183042), (0.972852213285, 0.211849583713, -0.0931575278038)124.573607609, 207.117044031, -176.383809185
52given(-0.992475243553, -0.121535146278, -0.0149029914068), (-0.105579732643, 0.911051536313, -0.398544876063), (0.0620146030275, -0.393972469089, -0.917027743643)436.241410137, 51.9721190182, 137.604770477
53given(-0.0636856731943, -0.176634530988, -0.982214018171), (-0.10489600335, -0.977575294433, 0.182601676323), (-0.992441919465, 0.114659435623, 0.0437292843699)297.06779619, 277.997181907, 239.49722595
54given(0.0250790080371, 0.20031157961, 0.979411208038), (0.234433673365, -0.953577668931, 0.189025083281), (0.971808569703, 0.224866405652, -0.0708745614485)129.455669218, 200.714354066, -180.386289942
55given(-0.996308479749, -0.0827042158853, -0.0230092558654), (-0.0696334033152, 0.935340437998, -0.34682770101), (0.0502056005185, -0.343945166734, -0.93764658585)432.304243215, 41.9920839088, 134.498982997
56given(-0.0789616528541, -0.14085187209, -0.986876794492), (-0.1594128514, -0.97544407043, 0.151975025159), (-0.984049084237, 0.169321042969, 0.0545690775131)295.530496095, 287.910742441, 231.864658474
57given(0.0500116831004, 0.214068670286, 0.975537511301), (0.241935847214, -0.950265226327, 0.196119977224), (0.969002516708, 0.226209204135, -0.099315248468)121.589848604, 198.065163512, -177.436827952
58given(-0.995673708128, -0.0901073088022, -0.0226834706815), (-0.076270565704, 0.931988709632, -0.354372467787), (0.0530722879563, -0.35110926792, -0.934829189869)431.575705529, 43.2010994534, 133.157182324
59given(-0.0866895303462, -0.130348697329, -0.987671069959), (-0.152064722984, -0.978054701938, 0.142426542611), (-0.984561448236, 0.162536817741, 0.0649656642133)296.059910416, 287.971740564, 233.015626247
60given(0.038520317682, 0.236423085523, 0.970886352648), (0.254808539174, -0.94181172194, 0.219233411641), (0.966223987225, 0.23894519256, -0.0965215077751)122.173859214, 193.11674007, -178.492577139
61given(0.017352437443, 0.188449468902, 0.981929575166), (0.232790629046, -0.955849932138, 0.179330505656), (0.972372056336, 0.225472182101, -0.0604555965614)129.607396846, 198.361114733, -177.773245793
62given(-0.0162193681033, -0.12365664378, -0.992192504783), (-0.157908400935, -0.97955303253, 0.124662718467), (-0.987320550284, 0.158697482369, -0.00363869167306)280.434926007, 290.908808746, 235.879207237

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Components

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Photosystem II ... , 6 types, 24 molecules A1a1A2a2B1b1B2b2C1c1C2c2D1d1D2d2O1o1O2o2U1u1U2u2

#1: Protein
Photosystem II protein D1 / / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38073.512 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19895, photosystem II
#2: Protein
Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56618.441 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19928
#3: Protein
Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 50515.613 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM46
#4: Protein
Photosystem II D2 protein / / PSII D2 protein / Photosystem Q(A) protein


Mass: 39341.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM47, photosystem II
#13: Protein
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO /


Mass: 35495.527 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#15: Protein
Photosystem II 12 kDa extrinsic protein, chloroplastic / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 16870.379 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9ZQS5

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Cytochrome b559 subunit ... , 2 types, 8 molecules E1e1E2e2F1f1F2f2

#5: Protein
Cytochrome b559 subunit alpha / / PSII reaction center subunit V


Mass: 9534.586 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM20
#6: Protein/peptide
Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 4958.928 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM21

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PHOTOSYSTEM II REACTION CENTER PROTEIN ... , 10 types, 38 molecules H1h1H2h2I1i1I2i2J1j1J2j2K1k1K2k2L1l1L2l2M1m1M2m2T1t1T2t2Y1y1...

#7: Protein
Photosystem II reaction center protein H / / PSII-H


Mass: 7498.996 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19925
#8: Protein/peptide
Photosystem II reaction center protein I / / PSII-I / PSII 4.8 kDa protein


Mass: 4472.214 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19882
#9: Protein/peptide
Photosystem II reaction center protein J / / PSII-J


Mass: 4089.821 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM23
#10: Protein/peptide
Photosystem II reaction center protein K / / PSII-K


Mass: 4703.714 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TLR0
#11: Protein/peptide
Photosystem II reaction center protein L / / PSII-L / PSII 5 kDa protein


Mass: 4379.130 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TM22
#12: Protein
PHOTOSYSTEM II REACTION CENTER PROTEIN M /


Mass: 11755.917 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#14: Protein/peptide
Photosystem II reaction center protein T / / PSII-T


Mass: 3732.606 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: O19927
#17: Protein/peptide
Photosystem II reaction center protein Ycf12 /


Mass: 4042.914 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q9TLX0
#18: Protein/peptide
PHOTOSYSTEM II REACTION CENTER PROTEIN X /


Mass: 4594.444 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#22: Protein Photosystem II reaction center protein Z /


Mass: 6483.804 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)

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Protein , 2 types, 6 molecules V1v1V2v2q1Q2

#16: Protein
Cytochrome c-550 / Cytochrome c550


Mass: 17240.738 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q76FB0
#21: Protein Extrinsic protein in photosystem II / Peripheral membrane protein


Mass: 24063.545 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote) / References: UniProt: Q76B86

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PEPTIDE CHAIN ... , 2 types, 8 molecules S1s1S2s2W1w1W2w2

#19: Protein/peptide
PEPTIDE CHAIN UNASSIGNED


Mass: 4302.190 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)
#20: Protein/peptide
PEPTIDE CHAIN UNASSIGNED


Mass: 2310.772 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cyanidium caldarium (eukaryote)

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Sugars , 2 types, 28 molecules

#34: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C51H96O15
#35: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 16 types, 343 molecules

#23: Chemical...
ChemComp-BCR / BETA-CAROTENE / Beta-Carotene


Mass: 536.873 Da / Num. of mol.: 38 / Source method: obtained synthetically / Formula: C40H56
#24: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#25: Chemical...
ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#26: Chemical
ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CaMn4O5
#27: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74N4O5
#28: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 52 / Source method: obtained synthetically
#29: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C45H86O10
#30: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#31: Chemical
ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#32: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#33: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#36: Chemical
ChemComp-PL9 / 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE / PLASTOQUINONE 9 / Plastoquinone


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2
#37: Chemical
ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H78O12S
#38: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#39: Chemical ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#40: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 6.1 / Details: PEG1450, glycerol, MES-NaOH, CaCl2, beta-DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.767→29.775 Å / Num. obs: 382176 / % possible obs: 99.4 % / Redundancy: 7.5 % / Biso Wilson estimate: 67.7883864741 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.43
Reflection shellResolution: 2.76→2.93 Å / Redundancy: 7.15 % / Rmerge(I) obs: 1.162 / Mean I/σ(I) obs: 2.04 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
SOLVEphasing
RefinementResolution: 2.77000368116→9.99956834485 Å / SU ML: 0.393299385627 / Cross valid method: THROUGHOUT / σ(F): 1.33646382975 / Phase error: 32.5479940329
RfactorNum. reflection% reflection
Rfree0.277700681274 18739 5.01470505592 %
Rwork0.249195678604 354942 -
Obs0.250629430593 373681 99.7464171411 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.5703747251 Å2
Refinement stepCycle: LAST / Resolution: 2.77000368116→9.99956834485 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms77709 0 15016 18 92743
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006149511692496131
X-RAY DIFFRACTIONf_angle_d1.18202202501132656
X-RAY DIFFRACTIONf_chiral_restr0.039276736384113466
X-RAY DIFFRACTIONf_plane_restr0.0049586553672716811
X-RAY DIFFRACTIONf_dihedral_angle_d15.429647774732055
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefinement-IDTypeRms dev position (Å)
11A12447X-RAY DIFFRACTIONPOSITIONAL0.011
12A22447X-RAY DIFFRACTIONPOSITIONAL0.011
13a12517X-RAY DIFFRACTIONPOSITIONAL0.011
14a22486X-RAY DIFFRACTIONPOSITIONAL0.01
21B13591X-RAY DIFFRACTIONPOSITIONAL0.009
22B23591X-RAY DIFFRACTIONPOSITIONAL0.009
23b13658X-RAY DIFFRACTIONPOSITIONAL0.011
24b23628X-RAY DIFFRACTIONPOSITIONAL0.009
31C13065X-RAY DIFFRACTIONPOSITIONAL0.011
32C23065X-RAY DIFFRACTIONPOSITIONAL0.011
33c13279X-RAY DIFFRACTIONPOSITIONAL0.01
34c23249X-RAY DIFFRACTIONPOSITIONAL0.009
41D12526X-RAY DIFFRACTIONPOSITIONAL0.009
42D22526X-RAY DIFFRACTIONPOSITIONAL0.009
43d12600X-RAY DIFFRACTIONPOSITIONAL0.01
44d22594X-RAY DIFFRACTIONPOSITIONAL0.008
51E1362X-RAY DIFFRACTIONPOSITIONAL0.011
52E2362X-RAY DIFFRACTIONPOSITIONAL0.011
53e1378X-RAY DIFFRACTIONPOSITIONAL0.01
54e2374X-RAY DIFFRACTIONPOSITIONAL0.006
61F1183X-RAY DIFFRACTIONPOSITIONAL0.01
62F2183X-RAY DIFFRACTIONPOSITIONAL0.01
63f1199X-RAY DIFFRACTIONPOSITIONAL0.008
64f2197X-RAY DIFFRACTIONPOSITIONAL0.008
71H1407X-RAY DIFFRACTIONPOSITIONAL0.007
72H2407X-RAY DIFFRACTIONPOSITIONAL0.007
73h1423X-RAY DIFFRACTIONPOSITIONAL0.009
74h2420X-RAY DIFFRACTIONPOSITIONAL0.006
81I1244X-RAY DIFFRACTIONPOSITIONAL0.007
82I2244X-RAY DIFFRACTIONPOSITIONAL0.007
83i1258X-RAY DIFFRACTIONPOSITIONAL0.008
84i2253X-RAY DIFFRACTIONPOSITIONAL0.008
91J1205X-RAY DIFFRACTIONPOSITIONAL0.008
92J2205X-RAY DIFFRACTIONPOSITIONAL0.008
93j1209X-RAY DIFFRACTIONPOSITIONAL0.009
94j2209X-RAY DIFFRACTIONPOSITIONAL0.008
101K1231X-RAY DIFFRACTIONPOSITIONAL0.015
102K2231X-RAY DIFFRACTIONPOSITIONAL0.015
103k1259X-RAY DIFFRACTIONPOSITIONAL0.008
104k2244X-RAY DIFFRACTIONPOSITIONAL0.014
111L1286X-RAY DIFFRACTIONPOSITIONAL0.01
112L2286X-RAY DIFFRACTIONPOSITIONAL0.01
113l1286X-RAY DIFFRACTIONPOSITIONAL0.01
114l2286X-RAY DIFFRACTIONPOSITIONAL0.01
121M1281X-RAY DIFFRACTIONPOSITIONAL0.01
122M2281X-RAY DIFFRACTIONPOSITIONAL0.01
123m1285X-RAY DIFFRACTIONPOSITIONAL0.01
124m2284X-RAY DIFFRACTIONPOSITIONAL0.012
131O11174X-RAY DIFFRACTIONPOSITIONAL0.067
132O21174X-RAY DIFFRACTIONPOSITIONAL0.067
133o11242X-RAY DIFFRACTIONPOSITIONAL0.019
134o21255X-RAY DIFFRACTIONPOSITIONAL0.03
141T1230X-RAY DIFFRACTIONPOSITIONAL0.008
142T2230X-RAY DIFFRACTIONPOSITIONAL0.008
143t1236X-RAY DIFFRACTIONPOSITIONAL0.009
144t2230X-RAY DIFFRACTIONPOSITIONAL0.008
151U1562X-RAY DIFFRACTIONPOSITIONAL0.055
152U2562X-RAY DIFFRACTIONPOSITIONAL0.055
153u1649X-RAY DIFFRACTIONPOSITIONAL0.009
154u2658X-RAY DIFFRACTIONPOSITIONAL0.014
161V1825X-RAY DIFFRACTIONPOSITIONAL0.017
162V2825X-RAY DIFFRACTIONPOSITIONAL0.017
163v1881X-RAY DIFFRACTIONPOSITIONAL0.009
164v2909X-RAY DIFFRACTIONPOSITIONAL0.01
171Y1147X-RAY DIFFRACTIONPOSITIONAL0.009
172Y2147X-RAY DIFFRACTIONPOSITIONAL0.009
173y1158X-RAY DIFFRACTIONPOSITIONAL0.014
174y2152X-RAY DIFFRACTIONPOSITIONAL0.015
181X1179X-RAY DIFFRACTIONPOSITIONAL0.009
182X2179X-RAY DIFFRACTIONPOSITIONAL0.009
183x1181X-RAY DIFFRACTIONPOSITIONAL0.015
184x2175X-RAY DIFFRACTIONPOSITIONAL0.018
191S1150X-RAY DIFFRACTIONPOSITIONAL0.008
192S2150X-RAY DIFFRACTIONPOSITIONAL0.008
193s1159X-RAY DIFFRACTIONPOSITIONAL0.006
194s2159X-RAY DIFFRACTIONPOSITIONAL0.006
201W1114X-RAY DIFFRACTIONPOSITIONAL0.007
202W2114X-RAY DIFFRACTIONPOSITIONAL0.007
203w1117X-RAY DIFFRACTIONPOSITIONAL0.007
204w2117X-RAY DIFFRACTIONPOSITIONAL0.005
211q1590X-RAY DIFFRACTIONPOSITIONAL0.013
212Q2590X-RAY DIFFRACTIONPOSITIONAL0.013
221Z2328X-RAY DIFFRACTIONPOSITIONAL0.007
222z2328X-RAY DIFFRACTIONPOSITIONAL0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2.77-2.80080.4025518948685960.37742469830111225X-RAY DIFFRACTION95.2461526066
2.8008-2.8330.3948788762116200.34030821142811763X-RAY DIFFRACTION99.8951274605
2.833-2.86680.3805361186956370.33424365443311785X-RAY DIFFRACTION99.9356395817
2.8668-2.90220.3743710414586330.32655416573911762X-RAY DIFFRACTION99.9032804062
2.9022-2.93940.3902938742255650.33265312122211823X-RAY DIFFRACTION99.9354630526
2.9394-2.97860.3656045343536180.31801586754111815X-RAY DIFFRACTION99.967837903
2.9786-3.020.3575024118126160.31029657840311769X-RAY DIFFRACTION99.9193223074
3.02-3.06380.3631901736486880.30778677298911739X-RAY DIFFRACTION99.9356654604
3.0638-3.11030.3434294367186430.29534743267411768X-RAY DIFFRACTION99.9436302142
3.1103-3.15970.3397944943626480.29911227117211794X-RAY DIFFRACTION99.943770584
3.1597-3.21240.3243135660796040.28179783823211806X-RAY DIFFRACTION99.9194847021
3.2124-3.26880.3208336141725910.27766750114111826X-RAY DIFFRACTION99.9597488327
3.2688-3.32940.3141407752446150.27485203129211839X-RAY DIFFRACTION99.9117529081
3.3294-3.39480.2972607674175970.25867402481211873X-RAY DIFFRACTION99.9198717949
3.3948-3.46560.3085210911876470.26266016090911727X-RAY DIFFRACTION99.9434617559
3.4656-3.54270.3014021689936090.26335317947511855X-RAY DIFFRACTION99.9759364723
3.5427-3.62720.2954728587356220.25664569500511856X-RAY DIFFRACTION99.9119224918
3.6272-3.72030.309747667446180.25547948485911813X-RAY DIFFRACTION99.9437208554
3.7203-3.82390.2868349142166280.24824335803611853X-RAY DIFFRACTION99.8559884791
3.8239-3.940.2665384022975970.24202180090811869X-RAY DIFFRACTION99.8158379374
3.94-4.07160.2725194233456180.23704265594211860X-RAY DIFFRACTION99.824
4.0716-4.22280.2642629328776190.23706988607511871X-RAY DIFFRACTION99.7603833866
4.2228-4.39930.2471630858826830.22905164614911766X-RAY DIFFRACTION99.7675909601
4.3993-4.60950.2497989688356010.22219919569911897X-RAY DIFFRACTION99.7207372537
4.6095-4.86680.2356992838956210.21997840278711900X-RAY DIFFRACTION99.7927791504
4.8668-5.19320.2535872899636400.22716348008211904X-RAY DIFFRACTION99.8885172798
5.1932-5.62950.2543484257566560.23850039588811936X-RAY DIFFRACTION99.9206475163
5.6295-6.26320.253245493226230.24466348417112024X-RAY DIFFRACTION99.976284585
6.2632-7.33390.2622985571896090.23023950370112077X-RAY DIFFRACTION99.976357475
7.3339-9.99960.2112190077866770.20582587372512147X-RAY DIFFRACTION99.9610258009

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