1S5L

Architecture of the photosynthetic oxygen evolving center


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.296 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1126/science.1093087
  • Structures With Same Primary Citation

  • 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 hav ...

    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.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
photosystem II core light harvesting proteinB, b510Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIQ1 (Thermosynechococcus elongatus (strain BP-1))
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Go to UniProtKB:  Q8DIQ1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
photosystem II CP43 proteinC, c473Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIF8 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 alpha subunitE, e84Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIP0 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Cytochrome b559 beta subunitF, f45Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIN9 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbH proteinH, h66Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DJ43 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center I proteinI, i38Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DJZ6 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center J proteinJ, j40Thermosynechococcus elongatusMutation(s): 0 
Find proteins for P59087 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center L proteinL, l37Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIN8 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center M proteinM, m36Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DHA7 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Photosystem II 12 kDa extrinsic proteinU, u134Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q9F1L5 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Cytochrome c-550V, v137Thermosynechococcus elongatusMutation(s): 0 
Find proteins for P0A386 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbX proteinX, x50Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q9F1R6 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Photosystem II PsbN proteinN, n37Thermosynechococcus elongatusMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center Z proteinZ, z62Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DHJ2 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem Q(B) proteinA, a344Thermosynechococcus elongatusMutation(s): 0 
EC: 1.10.3.9
Find proteins for P0A444 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Photosystem II reaction center protein KK, k37Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q9F1K9 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Photosystem II manganese-stabilizing polypeptideO, o246Thermosynechococcus elongatusMutation(s): 0 
Find proteins for P0A431 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
photosystem II PsbT proteinT, t32Thermosynechococcus elongatusMutation(s): 0 
Find proteins for Q8DIQ0 (Thermosynechococcus elongatus (strain BP-1))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
photosystem II reaction center D2 proteinD, d352Thermosynechococcus elongatusMutation(s): 0 
EC: 1.10.3.9
Find proteins for Q8CM25 (Thermosynechococcus elongatus (strain BP-1))
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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A, B, C, D, a, b, c, d
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
PHO
Query on PHO

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A, D, a, d
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
 Ligand Interaction
PL9
Query on PL9

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A, D, a, d
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
 Ligand Interaction
HEM
Query on HEM

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E, V, e, v
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
BCR
Query on BCR

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B, C, F, J, K, b, c, d, j, k
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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B, d
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
OEC
Query on OEC

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A, a
OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
 Ligand Interaction
BCT
Query on BCT

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A, D, a, d
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
FE
Query on FE

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A, a
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.342 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.296 
  • 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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Entry History 

Deposition Data

Revision History 

  • 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