9Z69 | pdb_00009z69

RT XFEL structure of the one-flash state of Photosystem II (1F, S2 rich) at 1.98 Angstrom obtained from conventional data at 9.5 keV

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 
    0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

High resolution structure of the S3 intermediate state in the water oxidation reaction of Photosystem II

Bhowmick, A.

To be published.

Macromolecule Content 

  • Total Structure Weight: 765.52 kDa 
  • Atom Count: 52,483 
  • Modeled Residue Count: 5,299 
  • Deposited Residue Count: 5,700 
  • Unique protein chains: 20

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
U [auth a]		344Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P0A444 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
V [auth b]		510Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
W [auth c]		461Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIF8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
X [auth d]		352Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for Q8CM25 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
Y [auth e]		84Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIP0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
Z [auth f]		45Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HAA [auth h],
G [auth H]		66Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJ43 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IBA [auth i],
H [auth I]		38Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JCA [auth j],
I [auth J]		40Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P59087 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KDA [auth k],
J [auth K]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1K9 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LEA [auth l],
K [auth L]		37Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIN8 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MFA [auth m],
L [auth M]		36Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHA7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideGA [auth o],
M [auth O]		272Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A431 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein THA [auth t],
N [auth T]		32Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinIA [auth u],
O [auth U]		134Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1L5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome c-550JA [auth v],
P [auth V]		163Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12KA [auth y],
Q [auth Y]		46Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DJI1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinLA [auth x],
R [auth X]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q9F1R6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth z],
S [auth Z]		62Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DHJ2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein YNA [auth r],
T [auth R]		41Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for Q8DKM3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Reference Sequence

Small Molecules

Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD


Download:Ideal Coordinates CCD File
AD [auth C]
AH [auth c]
BD [auth C]
BH [auth c]
CB [auth A]
AD [auth C],
AH [auth c],
BD [auth C],
BH [auth c],
CB [auth A],
CD [auth C],
ZD [auth H],
ZG [auth c],
ZH [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA


Download:Ideal Coordinates CCD File
CF [auth a]
FC [auth C]
GB [auth B]
GC [auth C]
GH [auth d]
CF [auth a],
FC [auth C],
GB [auth B],
GC [auth C],
GH [auth d],
HB [auth B],
HC [auth C],
HG [auth c],
HH [auth d],
IB [auth B],
IC [auth C],
IF [auth b],
IG [auth c],
JB [auth B],
JC [auth C],
JD [auth D],
JF [auth b],
JG [auth c],
KB [auth B],
KC [auth C],
KD [auth D],
KF [auth b],
KG [auth c],
LB [auth B],
LC [auth C],
LF [auth b],
LG [auth c],
MB [auth B],
MC [auth C],
MF [auth b],
MG [auth c],
NB [auth B],
NC [auth C],
NF [auth b],
NG [auth c],
OB [auth B],
OC [auth C],
OF [auth b],
OG [auth c],
PB [auth B],
PC [auth C],
PF [auth b],
PG [auth c],
QB [auth B],
QC [auth C],
QF [auth b],
QG [auth c],
RB [auth B],
RC [auth C],
RF [auth b],
RG [auth c],
SA [auth A],
SB [auth B],
SF [auth b],
SG [auth c],
TA [auth A],
TB [auth B],
TF [auth b],
TG [auth c],
UB [auth B],
UF [auth b],
VA [auth A],
VB [auth B],
VF [auth b],
WE [auth a],
WF [auth b],
XE [auth a],
XF [auth b],
ZA [auth A],
ZE [auth a]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


Download:Ideal Coordinates CCD File
FH [auth d],
ID [auth D],
UA [auth A],
YE [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD


Download:Ideal Coordinates CCD File
BB [auth A]
BC [auth B]
BG [auth b]
DF [auth a]
EF [auth a]
BB [auth A],
BC [auth B],
BG [auth b],
DF [auth a],
EF [auth a],
PD [auth D],
SD [auth D],
WH [auth f]
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


Download:Ideal Coordinates CCD File
CH [auth c]
DD [auth C]
DG [auth b]
DH [auth c]
FF [auth a]
CH [auth c],
DD [auth C],
DG [auth b],
DH [auth c],
FF [auth a],
GF [auth a],
JE [auth M],
JI [auth m],
ND [auth D],
OD [auth D],
PH [auth d],
VC [auth C],
YG [auth c],
ZB [auth B],
ZC [auth C]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9


Download:Ideal Coordinates CCD File
BF [auth a],
JH [auth d],
MD [auth D],
XA [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


Download:Ideal Coordinates CCD File
AB [auth A]
IE [auth L]
II [auth l]
LH [auth d]
MH [auth d]
AB [auth A],
IE [auth L],
II [auth l],
LH [auth d],
MH [auth d],
NH [auth d],
QD [auth D],
RD [auth D],
SH [auth e],
TD [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEC

Query on HEC


Download:Ideal Coordinates CCD File
PE [auth V],
PI [auth v]		HEME C
C34 H36 Fe N4 O4
YZTICFPLOXKSQO-RGGAHWMASA-L
HEM

Query on HEM


Download:Ideal Coordinates CCD File
VH [auth f],
XD [auth F]		PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR


Download:Ideal Coordinates CCD File
AF [auth a]
AG [auth b]
FE [auth K]
FI [auth k]
GE [auth K]
AF [auth a],
AG [auth b],
FE [auth K],
FI [auth k],
GE [auth K],
GI [auth k],
IH [auth d],
LD [auth D],
MI [auth t],
NE [auth T],
SC [auth C],
TC [auth C],
UG [auth c],
VG [auth c],
WA [auth A],
WB [auth B],
XB [auth B],
YB [auth B],
YD [auth H],
YF [auth b],
YH [auth h],
ZF [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX


Download:Ideal Coordinates CCD File
OA [auth A],
SE [auth a]		CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
STE

Query on STE


Download:Ideal Coordinates CCD File
AC [auth B]
AE [auth H]
AI [auth h]
BE [auth H]
BI [auth i]
AC [auth B],
AE [auth H],
AI [auth h],
BE [auth H],
BI [auth i],
CC [auth B],
CE [auth I],
CG [auth b],
CI [auth i],
DB [auth A],
DC [auth B],
DE [auth I],
DI [auth j],
EB [auth A],
EC [auth B],
ED [auth C],
EE [auth J],
EG [auth b],
EI [auth j],
FB [auth A],
FD [auth C],
FG [auth b],
GD [auth C],
GG [auth b],
HE [auth K],
HF [auth a],
HI [auth k],
KE [auth M],
KH [auth d],
KI [auth m],
LE [auth M],
LI [auth m],
ME [auth M],
NI [auth t],
OE [auth T],
OH [auth d],
OI [auth t],
QE [auth Z],
QH [auth d],
QI [auth z],
RE [auth R],
RH [auth e],
TH [auth e],
UC [auth C],
UD [auth D],
UH [auth e],
VD [auth E],
WC [auth C],
WD [auth E],
WG [auth c],
XC [auth C],
XG [auth c],
XH [auth f],
YA [auth A],
YC [auth C]
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
EH [auth d],
HD [auth D]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2


Download:Ideal Coordinates CCD File
PA [auth A],
TE [auth a]		FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
QA [auth A],
RA [auth A],
UE [auth a],
VE [auth a]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
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: 1.98 Å
  • R-Value Free:  0.213 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.547α = 90
b = 222.831β = 90
c = 309.126γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
cctbx.xfeldata reduction
cctbx.xfel.mergedata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM055302
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110501
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM126289
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM117126
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124169
German Research Foundation (DFG)GermanyUniCat
German Research Foundation (DFG)GermanySfb1078 TP A5
Swedish Research CouncilSweden2016-05183
Swedish Research CouncilSweden2020-03809
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393
Swedish Energy AgencySweden45421-1
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM139687
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10 OD023453
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169-01

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release