1S5L | pdb_00001s5l

Architecture of the photosynthetic oxygen evolving center

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.342 (Depositor) 
  • R-Value Work: 
    0.296 (Depositor), 0.309 (DCC) 
  • R-Value Observed: 
    0.296 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history. 

Literature

Architecture of the Photosynthetic Oxygen-Evolving Center

Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S.

(2004) Science 303: 1831-1838

  • DOI: https://doi.org/10.1126/science.1093087
  • Primary Citation Related Structures: 
    1S5L

  • PubMed Abstract: 

    Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). We report the structure of PSII of the cyanobacterium Thermosynechococcus elongatus at 3.5 angstrom resolution. We have assigned most of the amino acid residues of this 650-kilodalton dimeric multisubunit complex and refined the structure to reveal its molecular architecture. Consequently, we are able to describe details of the binding sites for cofactors and propose a structure of the oxygen-evolving center (OEC). The data strongly suggest that the OEC contains a cubane-like Mn3CaO4 cluster linked to a fourth Mn by a mono-micro-oxo bridge. The details of the surrounding coordination sphere of the metal cluster and the implications for a possible oxygen-evolving mechanism are discussed.

    • Organizational Affiliation: 
    • Department of Biological Sciences, Imperial College London, London, SW7 2AZ, UK.

Macromolecule Content 

  • Total Structure Weight: 692.75 kDa 
  • Atom Count: 45,945 
  • Modeled Residue Count: 5,130 
  • Deposited Residue Count: 5,520 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem Q(B) proteinA,
T [auth a]		344Thermosynechococcus vestitusMutation(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 core light harvesting proteinB,
U [auth b]		510Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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 proteinC,
V [auth c]		473Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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 reaction center D2 proteinD,
W [auth d]		352Thermosynechococcus vestitusMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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 alpha subunitE,
X [auth e]		84Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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 beta subunitF,
Y [auth f]		45Thermosynechococcus vestitusMutation(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 PsbH proteinG [auth H],
Z [auth h]		66Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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 I proteinAA [auth i],
H [auth I]		38Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DJZ6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center J proteinBA [auth j],
I [auth J]		40Thermosynechococcus vestitusMutation(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 KCA [auth k],
J [auth K]		37Thermosynechococcus vestitusMutation(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 L proteinDA [auth l],
K [auth L]		37Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
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 M proteinEA [auth m],
L [auth M]		36Thermosynechococcus vestitusMutation(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 polypeptideFA [auth o],
M [auth O]		246Thermosynechococcus vestitusMutation(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 PsbT proteinGA [auth t],
N [auth T]		32Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DIQ0 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinHA [auth u],
O [auth U]		134Thermosynechococcus vestitusMutation(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-550IA [auth v],
P [auth V]		137Thermosynechococcus vestitusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A386 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
photosystem II PsbX proteinJA [auth x],
Q [auth X]		50Thermosynechococcus vestitusMutation(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 PsbN proteinKA [auth n],
R [auth N]		37Thermosynechococcus vestitusMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center Z proteinLA [auth z],
S [auth Z]		62Thermosynechococcus vestitusMutation(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 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA

Query on CLA


Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth C]
AD [auth b]
AE [auth c]
BB [auth B]
AB [auth B],
AC [auth C],
AD [auth b],
AE [auth c],
BB [auth B],
BC [auth C],
BD [auth b],
BE [auth c],
CB [auth B],
CD [auth b],
DB [auth B],
DD [auth b],
EB [auth B],
ED [auth b],
FB [auth B],
FC [auth D],
FD [auth b],
FE [auth d],
GB [auth B],
GD [auth b],
GE [auth d],
HB [auth B],
HC [auth D],
HD [auth b],
IB [auth B],
ID [auth b],
IE [auth d],
JB [auth B],
JD [auth b],
KD [auth b],
LB [auth B],
LD [auth b],
OB [auth C],
OD [auth c],
PA [auth A],
PB [auth C],
PD [auth c],
QA [auth A],
QB [auth C],
QD [auth c],
RA [auth A],
RB [auth C],
RC [auth a],
RD [auth c],
SB [auth C],
SC [auth a],
SD [auth c],
TA [auth A],
TB [auth C],
TD [auth c],
UB [auth C],
UC [auth a],
UD [auth c],
VA [auth B],
VB [auth C],
VD [auth c],
WA [auth B],
WB [auth C],
WC [auth b],
WD [auth c],
XA [auth B],
XB [auth C],
XC [auth b],
XD [auth c],
YA [auth B],
YB [auth C],
YC [auth b],
YD [auth c],
ZA [auth B],
ZB [auth C],
ZC [auth b],
ZD [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO


Download:Ideal Coordinates CCD File
GC [auth D],
HE [auth d],
SA [auth A],
TC [auth a]		PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
PL9

Query on PL9


Download:Ideal Coordinates CCD File
IC [auth D],
JE [auth d],
UA [auth A],
VC [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
HEC

Query on HEC


Download:Ideal Coordinates CCD File
JC [auth E],
ME [auth e],
NC [auth V],
PE [auth v]		HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
BCR

Query on BCR


Download:Ideal Coordinates CCD File
CC [auth C]
CE [auth c]
DC [auth C]
DE [auth c]
KC [auth F]
CC [auth C],
CE [auth c],
DC [auth C],
DE [auth c],
KC [auth F],
LC [auth J],
LE [auth d],
MB [auth B],
MC [auth K],
MD [auth b],
NB [auth B],
ND [auth b],
NE [auth j],
OE [auth k]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT


Download:Ideal Coordinates CCD File
KB [auth B],
KE [auth d]		DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEC

Query on OEC


Download:Ideal Coordinates CCD File
OA [auth A],
QC [auth a]		OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-UHFFFAOYSA-N
BCT

Query on BCT


Download:Ideal Coordinates CCD File
EC [auth D],
EE [auth d],
NA [auth A],
PC [auth a]		BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE

Query on FE


Download:Ideal Coordinates CCD File
MA [auth A],
OC [auth a]		FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.342 (Depositor) 
  • R-Value Work:  0.296 (Depositor), 0.309 (DCC) 
  • R-Value Observed: 0.296 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.992α = 90
b = 228.849β = 90
c = 309.94γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-24
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description
  • Version 2.0: 2021-03-03
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary