1IZL

Crystal Structure of Photosystem II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Observed: 0.530

Literature

Macromolecules
Sequence Display for 1IZL

Classification: PHOTOSYNTHESIS

Total Structure Weight: 600355.56

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem II: Subunit PsbA A, J 360 Thermosynechococcus vulcanus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbA psbA-1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbB B, L 472 Thermosynechococcus elongatus Gene Name(s): psbB tlr1530
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbC C, M 473 Thermosynechococcus elongatus Gene Name(s): psbC tlr1631
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbD D, N 352 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbD1 tlr0455 psbD2 tlr1630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbE E, P 83 Thermosynechococcus elongatus Gene Name(s): psbE tsr1541
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbF F, Q 44 Thermosynechococcus elongatus Gene Name(s): psbF tsr1542
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbG G, R 220 Thermosynechococcus elongatus
Photosystem II: Subunit PsbH H, S 33 Thermosynechococcus elongatus
Photosystem II: Subunit PsbI I, T 26 Thermosynechococcus elongatus
Photosystem II: Subunit PsbK K, W 37 Thermosynechococcus elongatus Gene Name(s): psbK tsl0176
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbO O, Y 205 Thermosynechococcus elongatus
Photosystem II: Subunit PsbU U, Z 97 Thermosynechococcus elongatus
Photosystem II: Subunit PsbV 0, V 137 Thermosynechococcus vulcanus Gene Name(s): psbV
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II: Subunit PsbX 1, X 25 Thermosynechococcus elongatus

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem II


Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLA
Query on CLA

A, B, C, D, G, J, L, M, N, R, W CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHO
Query on PHO

A, D, J, N PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

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

D, K BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLA
Query on PLA

D, N 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL- PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-SUCCINIC ACID
N-PYRIDOXYL-2-METHYLASPARTIC ACID-5-MONOPHOSPHATE (Synonym)
C13 H19 N2 O9 P
ZFKRUCNEKPIDBK-ZDUSSCGKSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

D, N FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, J MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
1, B, C, G, H, I, L, M, O, R, S, T, U, X, Y, Z L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.7 Å
  • R-Value Observed: 0.530
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 129.38 α = 90.00
b = 225.19 β = 90.00
c = 308.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-04
  • Released Date: 2003-01-14
  • Deposition author(s): Kamiya, N., Shen, J.-R.

Revision History

  • 2008-04-27
    Type: Version format compliance
  • 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • 2012-11-28
    Type: Other