1S5L

Architecture of the photosynthetic oxygen evolving center

Structural Biology Knowledgebase: 1S5L SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.342
  • R-Value Work: 0.296

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1S5L

Classification: Photosynthesis

Total Structure Weight: 692748.75

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem Q(B) protein A, a 344 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbA1 psbA-1 tlr1843
photosystem II core light harvesting protein B, b 510 Thermosynechococcus elongatus Gene Name(s): psbB tlr1530
photosystem II CP43 protein C, c 473 Thermosynechococcus elongatus Gene Name(s): psbC tlr1631
photosystem II reaction center D2 protein D, d 352 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbD1 tlr0455 psbD2 tlr1630
Cytochrome b559 alpha subunit E, e 84 Thermosynechococcus elongatus Gene Name(s): psbE tsr1541
Cytochrome b559 beta subunit F, f 45 Thermosynechococcus elongatus Gene Name(s): psbF tsr1542
photosystem II PsbH protein H, h 66 Thermosynechococcus elongatus Gene Name(s): psbH tsl1386
Photosystem II reaction center I protein I, i 38 Thermosynechococcus elongatus Gene Name(s): psbI tsr1074
Photosystem II reaction center J protein J, j 40 Thermosynechococcus elongatus Gene Name(s): psbJ tsr1544
Photosystem II reaction center protein K K, k 37 Thermosynechococcus elongatus Gene Name(s): psbK tsl0176
Photosystem II reaction center L protein L, l 37 Thermosynechococcus elongatus Gene Name(s): psbL tsr1543
Photosystem II reaction center M protein M, m 36 Thermosynechococcus elongatus Gene Name(s): psbM tsl2052
Photosystem II manganese-stabilizing polypeptide O, o 246 Thermosynechococcus elongatus Gene Name(s): psbO tll0444
photosystem II PsbT protein T, t 32 Thermosynechococcus elongatus Gene Name(s): psbT tsr1531
Photosystem II 12 kDa extrinsic protein U, u 134 Thermosynechococcus elongatus Gene Name(s): psbU tll2409
Cytochrome c-550 V, v 137 Thermosynechococcus elongatus Gene Name(s): psbV tll1285
photosystem II PsbX protein X, x 50 Thermosynechococcus elongatus Gene Name(s): psbX tsr2013
Photosystem II PsbN protein N, n 37 Thermosynechococcus elongatus
Photosystem II reaction center Z protein Z, z 62 Thermosynechococcus elongatus Gene Name(s): psbZ tsr1967

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem II


Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLA
Query on CLA

A, B, C, D, a, b, c, d CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHO
Query on PHO

A, D, a, d PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PL9
Query on PL9

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
PLASTOQUINONE 9 (Synonym)
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

E, V, e, v PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

B, C, F, J, K, b, c, d, j, k BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

B, d DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OEC
Query on OEC

A, a OXYGEN EVOLVING SYSTEM
Ca Mn4 O4
UFRGXNUNWYSFQE-MBOUAFFSAW
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCT
Query on BCT

A, D, a, d BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, a FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
N, n L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.342
  • R-Value Work: 0.296
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 134.99 α = 90.00
b = 228.85 β = 90.00
c = 309.94 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-01-21
  • Released Date: 2004-02-24
  • Deposition author(s): Ferreira, K.N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S.

Revision History

  • 2012-07-25
    Type: Non-polymer description | Details: Change CLA to CL1
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4