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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 / chloroplast thylakoid membrane / phosphate ion binding / response to herbicide / respiratory electron transport chain / photosynthesis / extrinsic component of membrane / protein-chromophore linkage / oxidation-reduction process / protein stabilization / electron transfer activity / iron ion binding / calcium ion binding / heme binding / integral component of membrane / metal ion binding
Photosystem II cytochrome c-550 precursor / Twin-arginine translocation pathway, signal sequence / Photosystem II PsbT / Photosystem II PsbJ / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein ...Photosystem II cytochrome c-550 precursor / Twin-arginine translocation pathway, signal sequence / Photosystem II PsbT / Photosystem II PsbJ / Photosystem II PsbL / Photosystem II PsbI / Photosystem II PsbK / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II CP43 reaction centre protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Oxygen-evolving enhancer protein 3 / Photosystem antenna protein-like / Cytochrome c-like domain / Photosystem II reaction centre protein Ycf12 / Photosystem II PsbU, oxygen evolving complex / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Cytochrome c-like domain superfamily / Photosystem II CP47 reaction centre protein / Photosystem II PsbV, cytochrome c-550 precursor / PsbQ-like domain superfamily / Cytochrome c-550 domain / Photosystem antenna protein-like superfamily / Photosystem II reaction centre protein H / Photosynthetic reaction centre, L/M / Photosystem II reaction centre protein H superfamily / PsbL protein / Twin arginine translocation (Tat) signal profile. / Cytochrome c family profile. / Cytochrome b559 subunits heme-binding site signature. / Photosynthetic reaction center proteins signature. / Cytochrome c-550 domain / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II complex subunit Ycf12 / Oxygen evolving enhancer protein 3 (PsbQ) / Photosystem II 4 kDa reaction centre component / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / PsbJ / Photosystem II cytochrome b559, alpha subunit superfamily / Photosystem II reaction centre T protein / Photosystem II 10 kDa phosphoprotein / Photosystem II protein / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Photosynthetic reaction centre protein / Photosystem II PsbI superfamily / Photosystem II PsbK superfamily / Photosystem II PsbT superfamily / Photosystem II PsbJ superfamily / Photosystem II PsbL superfamily / Photosystem II protein D1/D2 superfamily
Photosystem II reaction center protein Ycf12 / 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 / Cytochrome b559 subunit alpha / Cytochrome c-550 / Photosystem II reaction center protein K / Extrinsic protein in photosystem II ...Photosystem II reaction center protein Ycf12 / 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 / Cytochrome b559 subunit alpha / Cytochrome c-550 / Photosystem II reaction center protein K / Extrinsic protein in photosystem II / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II protein D1 / Photosystem II reaction center protein I / Photosystem II 12 kDa extrinsic protein, chloroplastic
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
213chain O2 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
313chain o1 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
413chain o2 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
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:

Component-ID: 1

Dom-IDEns-IDSelection details
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 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
213chain O2 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
313chain o1 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
413chain o2 and (resseq -2:22 or resseq 39:54 or resseq 66:79 or resseq 101:130 or resseq 136:202 or resseq 214:231)
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 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:

Code: given

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

-
Components

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

#1: Protein/peptide
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/peptide
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/peptide
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/peptide
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/peptide
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/peptide
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/peptide
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

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

#7: Protein/peptide
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/peptide
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/peptide 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)

+
Protein/peptide , 2 types, 6 molecules V1v1V2v2q1Q2

#16: Protein/peptide
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/peptide 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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Non-polymers , 18 types, 371 molecules

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


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


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


Mass: 893.489 Da / Num. of mol.: 140 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Chlorophyll a
#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


Mass: 871.200 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C55H74N4O5 / Pheophytin
#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


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


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


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


Mass: 722.970 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid *YM
#34: Chemical
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


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


Mass: 510.615 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent *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


Mass: 749.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C53H80O2 / Plastoquinone
#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


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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.006149511692496131
f_angle_d1.18202202501132656
f_chiral_restr0.039276736384113466
f_plane_restr0.0049586553672716811
f_dihedral_angle_d15.429647774732055
Refine LS restraints NCS

Refinement-ID: X-RAY DIFFRACTION / Type: POSITIONAL

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A124470.011
12A224470.011
13a125170.011
14a224860.01
21B135910.009
22B235910.009
23b136580.011
24b236280.009
31C130650.011
32C230650.011
33c132790.01
34c232490.009
41D125260.009
42D225260.009
43d126000.01
44d225940.008
51E13620.011
52E23620.011
53e13780.01
54e23740.006
61F11830.01
62F21830.01
63f11990.008
64f21970.008
71H14070.007
72H24070.007
73h14230.009
74h24200.006
81I12440.007
82I22440.007
83i12580.008
84i22530.008
91J12050.008
92J22050.008
93j12090.009
94j22090.008
101K12310.015
102K22310.015
103k12590.008
104k22440.014
111L12860.01
112L22860.01
113l12860.01
114l22860.01
121M12810.01
122M22810.01
123m12850.01
124m22840.012
131O111740.067
132O211740.067
133o112420.019
134o212550.03
141T12300.008
142T22300.008
143t12360.009
144t22300.008
151U15620.055
152U25620.055
153u16490.009
154u26580.014
161V18250.017
162V28250.017
163v18810.009
164v29090.01
171Y11470.009
172Y21470.009
173y11580.014
174y21520.015
181X11790.009
182X21790.009
183x11810.015
184x21750.018
191S11500.008
192S21500.008
193s11590.006
194s21590.006
201W11140.007
202W21140.007
203w11170.007
204w21170.005
211q15900.013
212Q25900.013
221Z23280.007
222z23280.007
LS refinement shell

Refinement-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.77-2.80080.4025518948685960.3774246983011122595.2461526066
2.8008-2.8330.3948788762116200.3403082114281176399.8951274605
2.833-2.86680.3805361186956370.3342436544331178599.9356395817
2.8668-2.90220.3743710414586330.3265541657391176299.9032804062
2.9022-2.93940.3902938742255650.3326531212221182399.9354630526
2.9394-2.97860.3656045343536180.3180158675411181599.967837903
2.9786-3.020.3575024118126160.3102965784031176999.9193223074
3.02-3.06380.3631901736486880.3077867729891173999.9356654604
3.0638-3.11030.3434294367186430.2953474326741176899.9436302142
3.1103-3.15970.3397944943626480.2991122711721179499.943770584
3.1597-3.21240.3243135660796040.2817978382321180699.9194847021
3.2124-3.26880.3208336141725910.2776675011411182699.9597488327
3.2688-3.32940.3141407752446150.2748520312921183999.9117529081
3.3294-3.39480.2972607674175970.2586740248121187399.9198717949
3.3948-3.46560.3085210911876470.2626601609091172799.9434617559
3.4656-3.54270.3014021689936090.2633531794751185599.9759364723
3.5427-3.62720.2954728587356220.2566456950051185699.9119224918
3.6272-3.72030.309747667446180.2554794848591181399.9437208554
3.7203-3.82390.2868349142166280.2482433580361185399.8559884791
3.8239-3.940.2665384022975970.2420218009081186999.8158379374
3.94-4.07160.2725194233456180.2370426559421186099.824
4.0716-4.22280.2642629328776190.2370698860751187199.7603833866
4.2228-4.39930.2471630858826830.2290516461491176699.7675909601
4.3993-4.60950.2497989688356010.2221991956991189799.7207372537
4.6095-4.86680.2356992838956210.2199784027871190099.7927791504
4.8668-5.19320.2535872899636400.2271634800821190499.8885172798
5.1932-5.62950.2543484257566560.2385003958881193699.9206475163
5.6295-6.26320.253245493226230.2446634841711202499.976284585
6.2632-7.33390.2622985571896090.2302395037011207799.976357475
7.3339-9.99960.2112190077866770.2058258737251214799.9610258009

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