Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 
    0.291 (Depositor), 0.294 (DCC) 
  • R-Value Work: 
    0.281 (Depositor), 0.289 (DCC) 
  • R-Value Observed: 
    0.281 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser.

Kupitz, C.Basu, S.Grotjohann, I.Fromme, R.Zatsepin, N.A.Rendek, K.N.Hunter, M.S.Shoeman, R.L.White, T.A.Wang, D.James, D.Yang, J.H.Cobb, D.E.Reeder, B.Sierra, R.G.Liu, H.Barty, A.Aquila, A.L.Deponte, D.Kirian, R.A.Bari, S.Bergkamp, J.J.Beyerlein, K.R.Bogan, M.J.Caleman, C.Chao, T.C.Conrad, C.E.Davis, K.M.Fleckenstein, H.Galli, L.Hau-Riege, S.P.Kassemeyer, S.Laksmono, H.Liang, M.Lomb, L.Marchesini, S.Martin, A.V.Messerschmidt, M.Milathianaki, D.Nass, K.Ros, A.Roy-Chowdhury, S.Schmidt, K.Seibert, M.Steinbrener, J.Stellato, F.Yan, L.Yoon, C.Moore, T.A.Moore, A.L.Pushkar, Y.Williams, G.J.Boutet, S.Doak, R.B.Weierstall, U.Frank, M.Chapman, H.N.Spence, J.C.Fromme, P.

(2014) Nature 513: 261-265

  • DOI: https://doi.org/10.1038/nature13453
  • Primary Citation Related Structures: 
    4PBU, 4RVY

  • PubMed Abstract: 

    Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth's oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S0 to S4, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S1 state and after double laser excitation (putative S3 state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn4CaO5 core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the 'dangler' Mn) and the Mn3CaOx cubane in the S2 to S3 transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.


  • Organizational Affiliation
    • 1] Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA [2].

Macromolecule Content 

  • Total Structure Weight: 704.85 kDa 
  • Atom Count: 49,594 
  • Modeled Residue Count: 5,264 
  • Deposited Residue Count: 5,288 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1 1A,
B [auth a]
334Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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 proteinC [auth B],
D [auth b]
504Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinE [auth C],
F [auth c]
461Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinG [auth D],
H [auth d]
342Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaI [auth E],
J [auth e]
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaK [auth F],
L [auth f]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 HM [auth H],
N [auth h]
65Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IO [auth I],
P [auth i]
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 JQ [auth J],
R [auth j]
40Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 KS [auth K],
T [auth k]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 LU [auth L],
V [auth l]
37Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MW [auth M],
X [auth m]
34Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 polypeptideY [auth O],
Z [auth o]
243Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 TAA [auth T],
BA [auth t]
30Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinCA [auth U],
DA [auth u]
97Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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-550EA [auth V],
FA [auth v]
137Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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 X proteinGA [auth X],
HA [auth x]
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12IA [auth Y],
JA [auth y]
29Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
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: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZKA [auth Z],
LA [auth z]
62Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DHJ2 (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
DF [auth D]
OF [auth d]
PE [auth c]
QE [auth c]
RE [auth c]
DF [auth D],
OF [auth d],
PE [auth c],
QE [auth c],
RE [auth c],
VD [auth C],
WD [auth C],
XD [auth C],
XF [auth H],
ZF [auth h]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AC [auth B]
AD [auth b]
AE [auth c]
BC [auth B]
BE [auth c]
AC [auth B],
AD [auth b],
AE [auth c],
BC [auth B],
BE [auth c],
CB [auth a],
CC [auth B],
CE [auth c],
DB [auth a],
DC [auth B],
DE [auth c],
EC [auth B],
EE [auth c],
FE [auth c],
FF [auth d],
GB [auth a],
GD [auth C],
GE [auth c],
GF [auth d],
HD [auth C],
HE [auth c],
HF [auth d],
ID [auth C],
IE [auth c],
JD [auth C],
JE [auth c],
KD [auth C],
KE [auth c],
LC [auth b],
LD [auth C],
LE [auth c],
MC [auth b],
MD [auth C],
ME [auth c],
NC [auth b],
ND [auth C],
OA [auth A],
OC [auth b],
OD [auth C],
PA [auth A],
PB [auth B],
PC [auth b],
PD [auth C],
QB [auth B],
QC [auth b],
QD [auth C],
RB [auth B],
RC [auth b],
RD [auth C],
SA [auth A],
SB [auth B],
SC [auth b],
SD [auth C],
TB [auth B],
TC [auth b],
UB [auth B],
UC [auth b],
UE [auth D],
VB [auth B],
VC [auth b],
VE [auth D],
WB [auth B],
WC [auth b],
WE [auth D],
XB [auth B],
XC [auth b],
YB [auth B],
YC [auth b],
ZB [auth B],
ZC [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
EB [auth a],
FB [auth a],
QA [auth A],
RA [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
ED [auth b]
EF [auth D]
GG [auth L]
IB [auth a]
IG [auth l]
ED [auth b],
EF [auth D],
GG [auth L],
IB [auth a],
IG [auth l],
JG [auth l],
KC [auth b],
OB [auth B],
PF [auth d],
UA [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



Download:Ideal Coordinates CCD File
CD [auth b]
HC [auth B]
KF [auth d]
NB [auth a]
SE [auth c]
CD [auth b],
HC [auth B],
KF [auth d],
NB [auth a],
SE [auth c],
TE [auth c],
UG [auth Z],
VG [auth z],
YD [auth C],
ZA [auth A],
ZD [auth C],
ZE [auth D]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
BF [auth D],
MB [auth a],
MF [auth d],
YA [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
AF [auth D]
CF [auth D]
HG [auth L]
JF [auth d]
KG [auth l]
AF [auth D],
CF [auth D],
HG [auth L],
JF [auth d],
KG [auth l],
LF [auth d],
NF [auth d],
QF [auth E],
RF [auth e],
YE [auth D]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
SF [auth F],
SG [auth V],
TG [auth v],
UF [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
BD [auth b]
CG [auth K]
DG [auth K]
EG [auth k]
FC [auth B]
BD [auth b],
CG [auth K],
DG [auth K],
EG [auth k],
FC [auth B],
FD [auth b],
FG [auth k],
GC [auth B],
HB [auth a],
IF [auth d],
JC [auth B],
NE [auth c],
NG [auth T],
OE [auth c],
OG [auth T],
PG [auth t],
TA [auth A],
TD [auth C],
UD [auth C],
WF [auth H],
XE [auth D],
YF [auth h]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX

Query on OEX



Download:Ideal Coordinates CCD File
AB [auth a],
MA [auth A]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
LB [auth a],
XA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2

Query on FE2



Download:Ideal Coordinates CCD File
BB [auth a],
NA [auth A]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
DD [auth b]
IC [auth B]
LG [auth O]
MG [auth o]
TF [auth F]
DD [auth b],
IC [auth B],
LG [auth O],
MG [auth o],
TF [auth F],
VF [auth f]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
JB [auth a]
KB [auth a]
QG [auth U]
RG [auth u]
VA [auth A]
JB [auth a],
KB [auth a],
QG [auth U],
RG [auth u],
VA [auth A],
WA [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
AG [auth J],
BG [auth j]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free:  0.291 (Depositor), 0.294 (DCC) 
  • R-Value Work:  0.281 (Depositor), 0.289 (DCC) 
  • R-Value Observed: 0.281 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.61α = 90
b = 228.09β = 90
c = 308.68γ = 90
Software Package:
Software NamePurpose
Cheetahdata collection
PHASERphasing
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Data collection
  • Version 1.2: 2018-09-19
    Changes: Data collection
  • Version 2.0: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-11-27
    Changes: Structure summary