6JLM

XFEL structure of cyanobacterial photosystem II (dark state, dataset2)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history. 


Literature

An oxyl/oxo mechanism for oxygen-oxygen coupling in PSII revealed by an x-ray free-electron laser.

Suga, M., Akita, F., Yamashita, K., Nakajima, Y., Ueno, G., Li, H., Yamane, T., Hirata, K., Umena, Y., Yonekura, S., Yu, L.J., Murakami, H., Nomura, T., Kimura, T., Kubo, M., Baba, S., Kumasaka, T., Tono, K., Yabashi, M., Isobe, H., Yamaguchi, K., Yamamoto, M., Ago, H., Shen, J.R.

(2019) Science 366: 334-338

  • DOI: https://doi.org/10.1126/science.aax6998
  • Primary Citation of Related Structures:  
    6JLJ, 6JLK, 6JLL, 6JLM, 6JLN, 6JLO, 6JLP

  • PubMed Abstract: 

    Photosynthetic water oxidation is catalyzed by the Mn 4 CaO 5 cluster of photosystem II (PSII) with linear progression through five S-state intermediates (S 0 to S 4 ). To reveal the mechanism of water oxidation, we analyzed structures of PSII in the S 1 , S 2 , and S 3 states by x-ray free-electron laser serial crystallography. No insertion of water was found in S 2 , but flipping of D1 Glu 189 upon transition to S 3 leads to the opening of a water channel and provides a space for incorporation of an additional oxygen ligand, resulting in an open cubane Mn 4 CaO 6 cluster with an oxyl/oxo bridge. Structural changes of PSII between the different S states reveal cooperative action of substrate water access, proton release, and dioxygen formation in photosynthetic water oxidation.

    • Organizational Affiliation: 

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima Naka, Okayama 700-8530, Japan. michisuga@okayama-u.ac.jp ago@spring8.or.jp shen@cc.okayama-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
U [auth a]		344Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]		505Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		455Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		342Thermostichus vulcanusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		44Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		65Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		39Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for Q7DGD4 (Thermostichus vulcanus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P12312 (Thermostichus vulcanus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		244Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		104Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P56152 (Thermostichus vulcanus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		137Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A387 (Thermostichus vulcanus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]		30Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein XLA [auth x],
R [auth X]		40Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]		62Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0VWR5 (Thermostichus vulcanus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein YT [auth R]34Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0DM37 (Thermostichus vulcanus)
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD
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CI [auth c]
DI [auth c]
EI [auth c]
EJ [auth e]
FD [auth C]
CI [auth c],
DI [auth c],
EI [auth c],
EJ [auth e],
FD [auth C],
GD [auth C],
HD [auth C],
JE [auth H],
KJ [auth h],
XD [auth D]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA
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AD [auth C]
AI [auth c]
BD [auth C]
CD [auth C]
HB [auth B]
AD [auth C],
AI [auth c],
BD [auth C],
CD [auth C],
HB [auth B],
IB [auth B],
JB [auth B],
JG [auth b],
KB [auth B],
KG [auth b],
LB [auth B],
LG [auth b],
MB [auth B],
MG [auth b],
NB [auth B],
NG [auth b],
OB [auth B],
OG [auth b],
OH [auth c],
PB [auth B],
PF [auth a],
PG [auth b],
PH [auth c],
QB [auth B],
QC [auth C],
QF [auth a],
QG [auth b],
QH [auth c],
RA [auth A],
RB [auth B],
RC [auth C],
RG [auth b],
RH [auth c],
SA [auth A],
SB [auth B],
SC [auth C],
SF [auth a],
SG [auth b],
SH [auth c],
SI [auth d],
TA [auth A],
TB [auth B],
TC [auth C],
TD [auth D],
TG [auth b],
TH [auth c],
TI [auth d],
UB [auth B],
UC [auth C],
UD [auth D],
UG [auth b],
UH [auth c],
UI [auth d],
VA [auth A],
VB [auth B],
VC [auth C],
VG [auth b],
VH [auth c],
WB [auth B],
WC [auth C],
WG [auth b],
WH [auth c],
XC [auth C],
XG [auth b],
XH [auth c],
YC [auth C],
YG [auth b],
YH [auth c],
ZC [auth C],
ZH [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO
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QD [auth D],
RF [auth a],
RI [auth d],
UA [auth A]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD
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AB [auth A]
AC [auth B]
GE [auth F]
HJ [auth f]
MF [auth a]
AB [auth A],
AC [auth B],
GE [auth F],
HJ [auth f],
MF [auth a],
QE [auth L],
UF [auth a],
XA [auth A]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG
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BC [auth B]
CH [auth b]
DJ [auth d]
DK [auth z]
FB [auth A]
BC [auth B],
CH [auth b],
DJ [auth d],
DK [auth z],
FB [auth A],
FI [auth c],
GI [auth c],
HF [auth Y],
ID [auth C],
KF [auth Z],
LE [auth J],
VF [auth a]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9
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DB [auth A],
WD [auth D],
WI [auth d],
ZF [auth a]		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
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG
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CG [auth a]
DE [auth E]
MH [auth b]
OC [auth B]
PE [auth L]
CG [auth a],
DE [auth E],
MH [auth b],
OC [auth B],
PE [auth L],
XI [auth d],
YD [auth D],
YI [auth d],
ZD [auth D],
ZI [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM
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BF [auth V],
FE [auth F],
GJ [auth f],
XJ [auth v]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR
Query on BCR
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AH [auth b]
BH [auth b]
BI [auth c]
BK [auth y]
DD [auth C]
AH [auth b],
BH [auth b],
BI [auth c],
BK [auth y],
DD [auth C],
ED [auth C],
IE [auth H],
IF [auth Y],
JJ [auth h],
NI [auth c],
OE [auth K],
OJ [auth k],
TF [auth a],
VD [auth D],
VI [auth d],
VJ [auth t],
WA [auth A],
XB [auth B],
XE [auth T],
YB [auth B],
ZB [auth B],
ZG [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT
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BB [auth A]
BG [auth a]
DH [auth b]
EE [auth F]
FG [auth b]
BB [auth A],
BG [auth a],
DH [auth b],
EE [auth F],
FG [auth b],
FJ [auth e],
JD [auth C],
LF [auth a],
RE [auth M],
RJ [auth m],
SD [auth D],
SJ [auth m],
TE [auth M],
UJ [auth t]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX
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AG [auth a],
CB [auth A]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
HTG
Query on HTG
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CC [auth B]
CE [auth D]
CF [auth V]
CJ [auth d]
DC [auth B]
CC [auth B],
CE [auth D],
CF [auth V],
CJ [auth d],
DC [auth B],
EC [auth B],
EG [auth b],
EH [auth b],
FH [auth b],
GG [auth b],
HG [auth b],
HI [auth c],
II [auth c],
KD [auth C],
LC [auth B],
LD [auth C],
MC [auth B]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
GOL
Query on GOL
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AF [auth V]
AK [auth v]
DF [auth V]
DG [auth a]
EF [auth V]
AF [auth V],
AK [auth v],
DF [auth V],
DG [auth a],
EF [auth V],
FC [auth B],
FF [auth V],
GC [auth B],
GF [auth V],
GH [auth b],
HC [auth B],
HH [auth b],
IC [auth B],
IH [auth b],
JC [auth B],
JH [auth b],
JI [auth c],
KC [auth B],
KH [auth b],
KI [auth c],
MD [auth C],
ND [auth C],
OI [auth c],
PC [auth B],
PJ [auth l],
RD [auth D],
VE [auth O],
WE [auth T],
WF [auth a],
XF [auth a],
YA [auth A],
YE [auth T],
YJ [auth v],
ZA [auth A],
ZJ [auth v]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT
Query on BCT
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QA [auth A],
QI [auth d]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2
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NA [auth A],
PI [auth d]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA
Query on CA
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GB [auth B]
HE [auth F]
IG [auth b]
IJ [auth f]
MI [auth c]
GB [auth B],
HE [auth F],
IG [auth b],
IJ [auth f],
MI [auth c],
NH [auth c],
OD [auth C],
TJ [auth o],
UE [auth O]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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NF [auth a]
OA [auth A]
OF [auth a]
PA [auth A]
WJ [auth v]
NF [auth a],
OA [auth A],
OF [auth a],
PA [auth A],
WJ [auth v],
ZE [auth U]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
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NE [auth J],
NJ [auth j]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
UNL
Query on UNL
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AE [auth D]
AJ [auth d]
BE [auth D]
BJ [auth d]
CK [auth x]
AE [auth D],
AJ [auth d],
BE [auth D],
BJ [auth d],
CK [auth x],
EB [auth A],
JF [auth X],
KE [auth I],
LH [auth b],
LI [auth c],
LJ [auth i],
ME [auth J],
MJ [auth j],
NC [auth B],
PD [auth C],
QJ [auth m],
SE [auth M],
YF [auth a]
Unknown ligand
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME		BA [auth i],
H [auth I]		L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.04α = 90
b = 228.84β = 90
c = 286.98γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary
  • Version 2.0: 2023-11-22
    Changes: Advisory, Data collection, Database references, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Structure summary