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- PDB-7yq2: Crystal structure of photosystem II expressing psbA2 gene only -

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Basic information

Entry
Database: PDB / ID: 7yq2
TitleCrystal structure of photosystem II expressing psbA2 gene only
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 17
  • Cytochrome c-550
KeywordsPHOTOSYNTHESIS / ELECTRON TRANSPORT
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / membrane => GO:0016020 / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / (3R)-beta,beta-caroten-3-ol / Chem-SQD / Unknown ligand / Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 2 / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Y / Photosystem II reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNakajima, Y. / Suga, M. / Shen, J.R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03226 Japan
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Crystal structures of photosystem II from a cyanobacterium expressing psbA 2 in comparison to psbA 3 reveal differences in the D1 subunit.
Authors: Nakajima, Y. / Ugai-Amo, N. / Tone, N. / Nakagawa, A. / Iwai, M. / Ikeuchi, M. / Sugiura, M. / Suga, M. / Shen, J.R.
History
DepositionAug 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem II protein D1 2
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
J: Photosystem II reaction center protein J
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Photosystem II manganese-stabilizing polypeptide
T: Photosystem II reaction center protein T
U: Photosystem II 12 kDa extrinsic protein
V: Cytochrome c-550
Y: Photosystem II reaction center protein Ycf12
X: Photosystem II reaction center X protein
Z: Photosystem II reaction center protein Z
a: Photosystem II protein D1 2
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
j: Photosystem II reaction center protein J
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Photosystem II manganese-stabilizing polypeptide
t: Photosystem II reaction center protein T
u: Photosystem II 12 kDa extrinsic protein
v: Cytochrome c-550
y: Photosystem II reaction center protein Ycf12
x: Photosystem II reaction center X protein
z: Photosystem II reaction center protein Z
R: Photosystem II protein Y
hetero molecules


Theoretical massNumber of molelcules
Total (without water)793,817453
Polymers630,11239
Non-polymers163,705414
Water61,6113420
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.135, 228.172, 286.685
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
11(chain A and (resid 11 through 24 or resid 26...
21(chain a and ((resid 11 and (name CA or name...
12(chain B and (resid 2 through 35 or resid 37...
22(chain b and (resid 2 through 35 or resid 37...
13(chain C and (resid 23 through 134 or resid 136...
23(chain c and (resid 23 through 134 or resid 136...
14(chain D and (resid 11 through 125 or resid 127...
24(chain d and ((resid 11 through 12 and (name N...
15(chain E and (resid 6 or resid 8 through 11...
25(chain e and (resid 6 or resid 8 through 11...
16(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))
26(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))
17(chain H and (resid 2 or resid 4 through 201))
27(chain h and (resid 2 or resid 4 through 62...
18(chain I and (resid 1 or (resid 2 and (name...
28(chain i and (resid 1 through 37 or (resid 101...
19(chain J and (resid 5 through 40 or resid 101...
29(chain j and (resid 5 through 40 or resid 101 through 103))
110chain K
210chain k
111(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))
211(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))
112(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))
212(chain m and (resid 1 through 15 or resid 17...
113(chain O and (resid 4 through 48 or resid 50...
213(chain o and (resid 4 through 48 or resid 50...
114(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))
214(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))
115(chain U and resid 8 through 104)
215(chain u and ((resid 8 and (name N or name...
116(chain V and (resid 1 or resid 3 through 14...
216(chain v and (resid 1 or resid 3 through 14...
117(chain X and resid 2 through 40)
217(chain x and (resid 2 through 37 or (resid 38...
118(chain Y and (resid 17 through 29 or resid 31 through 46))
218(chain y and (resid 17 through 29 or resid 31...
119(chain Z and (resid 1 through 2 or (resid 3...
219(chain z and (resid 1 through 33 or (resid 34...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 11 through 24 or resid 26...A11 - 24
121(chain A and (resid 11 through 24 or resid 26...A26 - 67
131(chain A and (resid 11 through 24 or resid 26...A69 - 220
141(chain A and (resid 11 through 24 or resid 26...A222 - 228
151(chain A and (resid 11 through 24 or resid 26...A229
161(chain A and (resid 11 through 24 or resid 26...A11 - 344
171(chain A and (resid 11 through 24 or resid 26...A11 - 344
181(chain A and (resid 11 through 24 or resid 26...A11 - 344
191(chain A and (resid 11 through 24 or resid 26...A11 - 344
211(chain a and ((resid 11 and (name CA or name...a11
221(chain a and ((resid 11 and (name CA or name...a9 - 344
231(chain a and ((resid 11 and (name CA or name...a9 - 344
112(chain B and (resid 2 through 35 or resid 37...B2 - 35
122(chain B and (resid 2 through 35 or resid 37...B37 - 75
132(chain B and (resid 2 through 35 or resid 37...B77 - 120
142(chain B and (resid 2 through 35 or resid 37...B122 - 126
152(chain B and (resid 2 through 35 or resid 37...B127
162(chain B and (resid 2 through 35 or resid 37...B2 - 506
172(chain B and (resid 2 through 35 or resid 37...B2 - 506
182(chain B and (resid 2 through 35 or resid 37...B2 - 506
192(chain B and (resid 2 through 35 or resid 37...B2 - 506
212(chain b and (resid 2 through 35 or resid 37...b2 - 35
222(chain b and (resid 2 through 35 or resid 37...b37 - 75
232(chain b and (resid 2 through 35 or resid 37...b77 - 120
242(chain b and (resid 2 through 35 or resid 37...b122 - 147
252(chain b and (resid 2 through 35 or resid 37...b0
262(chain b and (resid 2 through 35 or resid 37...b2 - 505
272(chain b and (resid 2 through 35 or resid 37...b2 - 505
282(chain b and (resid 2 through 35 or resid 37...b2 - 505
292(chain b and (resid 2 through 35 or resid 37...b2 - 505
2102(chain b and (resid 2 through 35 or resid 37...b2 - 505
113(chain C and (resid 23 through 134 or resid 136...C23 - 134
123(chain C and (resid 23 through 134 or resid 136...C136 - 144
133(chain C and (resid 23 through 134 or resid 136...C146 - 200
143(chain C and (resid 23 through 134 or resid 136...C202 - 212
153(chain C and (resid 23 through 134 or resid 136...C214 - 377
163(chain C and (resid 23 through 134 or resid 136...C379 - 415
173(chain C and (resid 23 through 134 or resid 136...C417 - 470
183(chain C and (resid 23 through 134 or resid 136...C472 - 473
193(chain C and (resid 23 through 134 or resid 136...C502 - 513
1103(chain C and (resid 23 through 134 or resid 136...C515
1113(chain C and (resid 23 through 134 or resid 136...C517 - 518
213(chain c and (resid 23 through 134 or resid 136...c23 - 134
223(chain c and (resid 23 through 134 or resid 136...c136 - 144
233(chain c and (resid 23 through 134 or resid 136...c146 - 200
243(chain c and (resid 23 through 134 or resid 136...c202 - 212
253(chain c and (resid 23 through 134 or resid 136...c379 - 415
263(chain c and (resid 23 through 134 or resid 136...c472 - 913
273(chain c and (resid 23 through 134 or resid 136...c912
283(chain c and (resid 23 through 134 or resid 136...c917 - 918
114(chain D and (resid 11 through 125 or resid 127...D11 - 125
124(chain D and (resid 11 through 125 or resid 127...D127 - 232
134(chain D and (resid 11 through 125 or resid 127...D233 - 234
144(chain D and (resid 11 through 125 or resid 127...D11 - 352
154(chain D and (resid 11 through 125 or resid 127...D11 - 352
164(chain D and (resid 11 through 125 or resid 127...D11 - 352
174(chain D and (resid 11 through 125 or resid 127...D11 - 352
214(chain d and ((resid 11 through 12 and (name N...d11 - 12
224(chain d and ((resid 11 through 12 and (name N...d11 - 352
234(chain d and ((resid 11 through 12 and (name N...d11 - 352
244(chain d and ((resid 11 through 12 and (name N...d11 - 352
254(chain d and ((resid 11 through 12 and (name N...d11 - 352
115(chain E and (resid 6 or resid 8 through 11...E6
125(chain E and (resid 6 or resid 8 through 11...E8 - 11
135(chain E and (resid 6 or resid 8 through 11...E13 - 58
145(chain E and (resid 6 or resid 8 through 11...E59 - 60
155(chain E and (resid 6 or resid 8 through 11...E3 - 201
165(chain E and (resid 6 or resid 8 through 11...E3 - 201
175(chain E and (resid 6 or resid 8 through 11...E3 - 201
215(chain e and (resid 6 or resid 8 through 11...e6
225(chain e and (resid 6 or resid 8 through 11...e8 - 11
235(chain e and (resid 6 or resid 8 through 11...e13 - 59
245(chain e and (resid 6 or resid 8 through 11...e60
255(chain e and (resid 6 or resid 8 through 11...e6 - 84
265(chain e and (resid 6 or resid 8 through 11...e6 - 84
275(chain e and (resid 6 or resid 8 through 11...e6 - 84
285(chain e and (resid 6 or resid 8 through 11...e6 - 84
116(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F14 - 43
126(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F45
136(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F101
146(chain F and (resid 14 through 43 or resid 45 or resid 101 or resid 103))F103
216(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f14 - 43
226(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f45
236(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f101
246(chain f and (resid 14 through 43 or resid 45 or resid 101 or resid 103))f103
117(chain H and (resid 2 or resid 4 through 201))H0
217(chain h and (resid 2 or resid 4 through 62...h2
227(chain h and (resid 2 or resid 4 through 62...h4 - 62
237(chain h and (resid 2 or resid 4 through 62...h63
247(chain h and (resid 2 or resid 4 through 62...h2 - 66
257(chain h and (resid 2 or resid 4 through 62...h2 - 66
267(chain h and (resid 2 or resid 4 through 62...h2 - 66
277(chain h and (resid 2 or resid 4 through 62...h2 - 66
287(chain h and (resid 2 or resid 4 through 62...h2 - 66
118(chain I and (resid 1 or (resid 2 and (name...I1
128(chain I and (resid 1 or (resid 2 and (name...I2
138(chain I and (resid 1 or (resid 2 and (name...I1 - 37
148(chain I and (resid 1 or (resid 2 and (name...I1 - 37
158(chain I and (resid 1 or (resid 2 and (name...I1 - 37
168(chain I and (resid 1 or (resid 2 and (name...I1 - 37
218(chain i and (resid 1 through 37 or (resid 101...i0
119(chain J and (resid 5 through 40 or resid 101...J5 - 40
129(chain J and (resid 5 through 40 or resid 101...J101 - 102
139(chain J and (resid 5 through 40 or resid 101...J103
149(chain J and (resid 5 through 40 or resid 101...J5 - 40
159(chain J and (resid 5 through 40 or resid 101...J5 - 40
169(chain J and (resid 5 through 40 or resid 101...J5 - 40
179(chain J and (resid 5 through 40 or resid 101...J5 - 40
189(chain J and (resid 5 through 40 or resid 101...J5 - 40
219(chain j and (resid 5 through 40 or resid 101 through 103))j5 - 40
229(chain j and (resid 5 through 40 or resid 101 through 103))j101 - 103
1110chain KK10 - 46
2110chain kk10 - 46
1111(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L1 - 7
1211(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L9 - 23
1311(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L25 - 37
1411(chain L and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))L101
2111(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l1 - 7
2211(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l9 - 23
2311(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l25 - 37
2411(chain l and (resid 1 through 7 or resid 9 through 23 or resid 25 through 37 or resid 101))l101
1112(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M1 - 15
1212(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M17 - 34
1312(chain M and (resid 1 through 15 or resid 17 through 34 or resid 101 through 102))M101 - 102
2112(chain m and (resid 1 through 15 or resid 17...m1 - 15
2212(chain m and (resid 1 through 15 or resid 17...m17 - 32
2312(chain m and (resid 1 through 15 or resid 17...m33
2412(chain m and (resid 1 through 15 or resid 17...m1 - 34
2512(chain m and (resid 1 through 15 or resid 17...m34
2612(chain m and (resid 1 through 15 or resid 17...m1 - 34
1113(chain O and (resid 4 through 48 or resid 50...O4 - 48
1213(chain O and (resid 4 through 48 or resid 50...O50 - 68
1313(chain O and (resid 4 through 48 or resid 50...O70 - 73
1413(chain O and (resid 4 through 48 or resid 50...O75
1513(chain O and (resid 4 through 48 or resid 50...O100 - 17190
1613(chain O and (resid 4 through 48 or resid 50...O1919795
1713(chain O and (resid 4 through 48 or resid 50...O197 - 216
1813(chain O and (resid 4 through 48 or resid 50...O2 - 216
1913(chain O and (resid 4 through 48 or resid 50...O218 - 246
11013(chain O and (resid 4 through 48 or resid 50...O301
2113(chain o and (resid 4 through 48 or resid 50...o4 - 48
2213(chain o and (resid 4 through 48 or resid 50...o50 - 61
2313(chain o and (resid 4 through 48 or resid 50...o62 - 63
2413(chain o and (resid 4 through 48 or resid 50...o4 - 246
2513(chain o and (resid 4 through 48 or resid 50...o4 - 246
2613(chain o and (resid 4 through 48 or resid 50...o4 - 246
2713(chain o and (resid 4 through 48 or resid 50...o4 - 246
1114(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T1 - 24
1214(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T26 - 30
1314(chain T and (resid 1 through 24 or resid 26 through 30 or resid 101))T101
2114(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t1 - 24
2214(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t26 - 30
2314(chain t and (resid 1 through 24 or resid 26 through 30 or resid 101))t101
1115(chain U and resid 8 through 104)U8 - 104
2115(chain u and ((resid 8 and (name N or name...u8
2215(chain u and ((resid 8 and (name N or name...u8 - 104
2315(chain u and ((resid 8 and (name N or name...u8 - 104
2415(chain u and ((resid 8 and (name N or name...u8 - 104
2515(chain u and ((resid 8 and (name N or name...u8 - 104
1116(chain V and (resid 1 or resid 3 through 14...V1
1216(chain V and (resid 1 or resid 3 through 14...V3 - 14
1316(chain V and (resid 1 or resid 3 through 14...V16
1416(chain V and (resid 1 or resid 3 through 14...V17
1516(chain V and (resid 1 or resid 3 through 14...V1 - 137
1616(chain V and (resid 1 or resid 3 through 14...V1 - 137
1716(chain V and (resid 1 or resid 3 through 14...V1 - 137
2116(chain v and (resid 1 or resid 3 through 14...v1
2216(chain v and (resid 1 or resid 3 through 14...v3 - 14
2316(chain v and (resid 1 or resid 3 through 14...v16 - 54
2416(chain v and (resid 1 or resid 3 through 14...v56 - 105
2516(chain v and (resid 1 or resid 3 through 14...v107 - 137
2616(chain v and (resid 1 or resid 3 through 14...v201
1117(chain X and resid 2 through 40)X2 - 40
2117(chain x and (resid 2 through 37 or (resid 38...x2 - 37
2217(chain x and (resid 2 through 37 or (resid 38...x38
2317(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2417(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2517(chain x and (resid 2 through 37 or (resid 38...x2 - 40
2617(chain x and (resid 2 through 37 or (resid 38...x2 - 40
1118(chain Y and (resid 17 through 29 or resid 31 through 46))Y17 - 29
1218(chain Y and (resid 17 through 29 or resid 31 through 46))Y31 - 46
2118(chain y and (resid 17 through 29 or resid 31...y17 - 29
2218(chain y and (resid 17 through 29 or resid 31...y31 - 42
2318(chain y and (resid 17 through 29 or resid 31...y43
2418(chain y and (resid 17 through 29 or resid 31...y17 - 46
2518(chain y and (resid 17 through 29 or resid 31...y17 - 46
2618(chain y and (resid 17 through 29 or resid 31...y17 - 46
2718(chain y and (resid 17 through 29 or resid 31...y17 - 46
1119(chain Z and (resid 1 through 2 or (resid 3...Z1 - 2
1219(chain Z and (resid 1 through 2 or (resid 3...Z3
1319(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1419(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1519(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
1619(chain Z and (resid 1 through 2 or (resid 3...Z1 - 62
2119(chain z and (resid 1 through 33 or (resid 34...z1 - 33
2219(chain z and (resid 1 through 33 or (resid 34...z34 - 35
2319(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2419(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2519(chain z and (resid 1 through 33 or (resid 34...z1 - 62
2619(chain z and (resid 1 through 33 or (resid 34...z1 - 62

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

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Components

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Photosystem II ... , 17 types, 33 molecules AaBbCcDdHhIiJjKkLlMmOoTtUuYyXx...

#1: Protein Photosystem II protein D1 2 / / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39762.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A446, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / / PSII 47 kDa protein / Protein CP-47


Mass: 56656.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 reaction center protein / / PSII 43 kDa protein / Protein CP-43


Mass: 50287.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / / PSII D2 protein / Photosystem II Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / / PSII-H


Mass: 7358.754 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / / PSII-I / PSII 4.4 kDa protein


Mass: 4438.255 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein J / / PSII-J


Mass: 4105.908 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P59087
#10: Protein/peptide Photosystem II reaction center protein K / / PSII-K


Mass: 5028.083 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1K9
#11: Protein/peptide Photosystem II reaction center protein L / / PSII-L


Mass: 4299.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN8
#12: Protein/peptide Photosystem II reaction center protein M / / PSII-M


Mass: 4009.682 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHA7
#13: Protein Photosystem II manganese-stabilizing polypeptide / / MSP


Mass: 29637.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A431
#14: Protein/peptide Photosystem II reaction center protein T / / PSII-T / PSII-Tc


Mass: 3906.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIQ0
#15: Protein Photosystem II 12 kDa extrinsic protein / / PS II complex 12 kDa extrinsic protein / PSII-U


Mass: 15030.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1L5
#17: Protein/peptide Photosystem II reaction center protein Ycf12 /


Mass: 5039.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DJI1
#18: Protein/peptide Photosystem II reaction center X protein /


Mass: 4322.226 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q9F1R6
#19: Protein Photosystem II reaction center protein Z / / PSII-Z


Mass: 6794.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DHJ2
#20: Protein/peptide Photosystem II protein Y /


Mass: 4590.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DKM3

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

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


Mass: 9580.840 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: Q8DIN9

-
Protein , 1 types, 2 molecules Vv

#16: Protein Cytochrome c-550 / Cytochrome c-549 / Cytochrome c550 / Low-potential cytochrome c


Mass: 18046.943 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus vestitus BP-1 (bacteria)
References: UniProt: P0A386

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Sugars , 3 types, 60 molecules

#31: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#36: Sugar...
ChemComp-HTG / heptyl 1-thio-beta-D-glucopyranoside / HEPTYL 1-THIOHEXOPYRANOSIDE / heptyl 1-thio-beta-D-glucoside / heptyl 1-thio-D-glucoside / heptyl 1-thio-glucoside


Type: D-saccharide / Mass: 294.408 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C13H26O5S / Comment: detergent*YM
#37: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharideCarbohydrate / Mass: 949.299 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C51H96O15

-
Non-polymers , 20 types, 3774 molecules

#21: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5
#22: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#23: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#25: Chemical
ChemComp-PHO / PHEOPHYTIN A / Pheophytin


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical
ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56
#27: 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.: 8 / Source method: obtained synthetically / Formula: C41H78O12S
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10
#29: 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 / Feature type: SUBJECT OF INVESTIGATION
#30: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 258.120 Da / Num. of mol.: 77 / Source method: obtained synthetically
#32: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#33: Chemical ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#34: Chemical...
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 116 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#35: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#38: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#39: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#40: Chemical ChemComp-RRX / (3R)-beta,beta-caroten-3-ol / beta-Cryptoxanthin / Β-Cryptoxanthin


Mass: 552.872 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H56O
#41: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#42: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C34H34FeN4O4
#43: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3420 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.69 %
Crystal growTemperature: 285 K / Method: microbatch / pH: 6
Details: 5% PEG 1450, 20mM NaCl, 10mM CaCl2, 40mM MgSO4, 20mM Mes BUFFER, pH 6.0, MICRO-BATCH METHOD UNDER OIL, TEMPARATURE 285K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 621644 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 32.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rrim(I) all: 0.1 / Χ2: 0.855 / Net I/σ(I): 11.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-2.014.8071.2971.35955640.6611.45399.7
2.01-2.15.0240.82.3640890.8380.89199.8
2.1-2.34.8670.4933.81091880.9260.55199.8
2.3-2.54.9130.2886.3769980.9720.32199.8
2.5-34.9660.1411.461146500.9920.15699.8
3-44.940.05822.83915170.9980.06599.9
4-54.6850.03932.61327490.9980.04499.6

-
Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PHENIX1.17.1_3660refinement
REFMAC5.8.0103refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WU2

3wu2


Resolution: 1.9→20 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 31121 5.01 %
Rwork0.1512 590250 -
obs0.1528 621333 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.55 Å2 / Biso mean: 46.2203 Å2 / Biso min: 18.94 Å2
Refinement stepCycle: final / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41169 0 10640 3468 55277
Biso mean--56.88 53.34 -
Num. residues----5302
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3073X-RAY DIFFRACTION11.22TORSIONAL
12a3073X-RAY DIFFRACTION11.22TORSIONAL
21B5814X-RAY DIFFRACTION11.22TORSIONAL
22b5814X-RAY DIFFRACTION11.22TORSIONAL
31C5157X-RAY DIFFRACTION11.22TORSIONAL
32c5157X-RAY DIFFRACTION11.22TORSIONAL
41D3292X-RAY DIFFRACTION11.22TORSIONAL
42d3292X-RAY DIFFRACTION11.22TORSIONAL
51E648X-RAY DIFFRACTION11.22TORSIONAL
52e648X-RAY DIFFRACTION11.22TORSIONAL
61F298X-RAY DIFFRACTION11.22TORSIONAL
62f298X-RAY DIFFRACTION11.22TORSIONAL
71H0X-RAY DIFFRACTION11.22TORSIONAL
72h0X-RAY DIFFRACTION11.22TORSIONAL
81I378X-RAY DIFFRACTION11.22TORSIONAL
82i378X-RAY DIFFRACTION11.22TORSIONAL
91J334X-RAY DIFFRACTION11.22TORSIONAL
92j334X-RAY DIFFRACTION11.22TORSIONAL
101K428X-RAY DIFFRACTION11.22TORSIONAL
102k428X-RAY DIFFRACTION11.22TORSIONAL
111L412X-RAY DIFFRACTION11.22TORSIONAL
112l412X-RAY DIFFRACTION11.22TORSIONAL
121M386X-RAY DIFFRACTION11.22TORSIONAL
122m386X-RAY DIFFRACTION11.22TORSIONAL
131O2156X-RAY DIFFRACTION11.22TORSIONAL
132o2156X-RAY DIFFRACTION11.22TORSIONAL
141T312X-RAY DIFFRACTION11.22TORSIONAL
142t312X-RAY DIFFRACTION11.22TORSIONAL
151U926X-RAY DIFFRACTION11.22TORSIONAL
152u926X-RAY DIFFRACTION11.22TORSIONAL
161V1256X-RAY DIFFRACTION11.22TORSIONAL
162v1256X-RAY DIFFRACTION11.22TORSIONAL
171X341X-RAY DIFFRACTION11.22TORSIONAL
172x341X-RAY DIFFRACTION11.22TORSIONAL
181Y250X-RAY DIFFRACTION11.22TORSIONAL
182y250X-RAY DIFFRACTION11.22TORSIONAL
191Z517X-RAY DIFFRACTION11.22TORSIONAL
192z517X-RAY DIFFRACTION11.22TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.920.32629960.30461929098
1.92-1.940.299810150.278319576100
1.94-1.970.296410510.267719521100
1.97-1.990.286110730.256619484100
1.99-2.020.288910560.247319503100
2.02-2.050.254610440.225219524100
2.05-2.080.247310280.212119626100
2.08-2.110.261710320.209219611100
2.11-2.140.24389840.200319585100
2.14-2.170.231410350.187919543100
2.17-2.210.22369960.183719630100
2.21-2.250.23119870.18519592100
2.25-2.30.21510180.17319654100
2.3-2.340.204410720.161419568100
2.34-2.390.199910210.153219649100
2.39-2.450.19319760.155219665100
2.45-2.510.186410440.146119625100
2.51-2.580.184310800.144619591100
2.58-2.650.184210300.143419695100
2.65-2.740.187610640.139619634100
2.74-2.840.183810040.138119745100
2.84-2.950.177110490.138819667100
2.95-3.080.189810260.138319807100
3.08-3.250.16510940.136119672100
3.25-3.450.163510470.129519775100
3.45-3.710.160510360.129119837100
3.71-4.080.159610550.125719844100
4.08-4.670.147410520.121719858100
4.67-5.860.160610420.131920073100
Refinement TLS params.Method: refined / Origin x: -13.169 Å / Origin y: -13.3638 Å / Origin z: 25.7906 Å
111213212223313233
T0.2693 Å20.0369 Å2-0.0141 Å2-0.2143 Å2-0.0305 Å2--0.1714 Å2
L0.129 °20.051 °2-0.0081 °2-0.2863 °2-0.1232 °2--0.3816 °2
S-0.0021 Å °0.0165 Å °-0.0075 Å °0.0042 Å °0.0397 Å °0.0156 Å °-0.0418 Å °0.0005 Å °-0.0371 Å °
Refinement TLS groupSelection details: all

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