4YUU

Crystal structure of oxygen-evolving photosystem II from a red alga


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.249

Literature

Macromolecules
Sequence Display for 4YUU

Classification: PHOTOSYNTHESIS

Total Structure Weight: 1579524.13

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem II protein D1 A1, A2, a1, a2 344 Cyanidium caldarium EC#: 1.10.3.9 IUBMB
Gene Name(s): psbA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II CP47 reaction center protein B1, B2, b1, b2 509 Cyanidium caldarium Gene Name(s): psbB
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II CP43 reaction center protein C1, C2, c1, c2 460 Cyanidium caldarium Gene Name(s): psbC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II D2 protein D1, D2, d1, d2 351 Cyanidium caldarium EC#: 1.10.3.9 IUBMB
Gene Name(s): psbD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 subunit alpha E1, E2, e1, e2 84 Cyanidium caldarium Gene Name(s): psbE
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 subunit beta F1, F2, f1, f2 43 Cyanidium caldarium Gene Name(s): psbF
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein H H1, H2, h1, h2 67 Cyanidium caldarium Gene Name(s): psbH
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein I I1, I2, i1, i2 38 Cyanidium caldarium Gene Name(s): psbI
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein J J1, J2, j1, j2 39 Cyanidium caldarium Gene Name(s): psbJ
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein K K1, K2, k1, k2 41 Cyanidium caldarium Gene Name(s): psbK
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein L L1, L2, l1, l2 38 Cyanidium caldarium Gene Name(s): psbL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM II REACTION CENTER PROTEIN M M1, M2, m1, m2 108 Cyanidium caldarium
PHOTOSYSTEM II MANGANESE-STABILIZING POLYPEPTIDE, PSBO O1, O2, o1, o2 329 Cyanidium caldarium
Photosystem II reaction center protein T T1, T2, t1, t2 32 Cyanidium caldarium Gene Name(s): psbT
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II 12 kDa extrinsic protein, chloroplastic U1, U2, u1, u2 155 Cyanidium caldarium Gene Name(s): psbU
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c-550 V1, V2, v1, v2 155 Cyanidium caldarium Gene Name(s): psbV
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein Ycf12 Y1, Y2, y1, y2 35 Cyanidium caldarium Gene Name(s): ycf12 ycf34
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM II REACTION CENTER PROTEIN X X1, X2, x1, x2 40 Cyanidium caldarium
PEPTIDE CHAIN UNASSIGNED S1, S2, s1, s2 46 Cyanidium caldarium
PEPTIDE CHAIN UNASSIGNED W1, W2, w1, w2 25 Cyanidium caldarium
Extrinsic protein in photosystem II Q2, q1 218 Cyanidium caldarium Gene Name(s): psbQ'
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein Z Z2, z2 62 Cyanidium caldarium

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem II from a red alga


Small Molecules
Ligands 17 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGD
Query on DGD

C1, C2, H1, H2, c1, c2, h1, h2 DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CLA
Query on CLA

A1, A2, B1, B2, C1, C2, D1, D2, K2, a1, a2, b1, b2, c1, c2, d1, d2 CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PHO
Query on PHO

A1, A2, D1, D2, a1, a2, d1, d2 PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SQD
Query on SQD

B2, D1, D2, b2 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA- D-GLUCOPYRANOSYL]-SN-GLYCEROL
SULFOQUINOVOSYLDIACYLGLYCEROL (Synonym)
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMG
Query on LMG

A1, A2, B1, B2, C1, C2, D1, F2, I2, M1, a1, a2, b1, b2, c1, c2, d1, d2, j2 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PL9
Query on PL9

D1, D2, d1, d2 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LHG
Query on LHG

A2, B1, B2, D1, D2, L1, L2, a1, a2, b1, b2, d1, d2, l1, l2 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

E1, E2, V1, V2, e2, f1, v1, v2 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

A1, A2, B1, B2, C1, C2, D1, F2, H1, H2, J1, K1, K2, a1, a2, b1, b2, c1, c2, d1, d2, h1, h2, j2, k1, k2, z2 BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

C1, L1, M1, T1, a2, b2, c1, i2, l1, m1, m2 DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
OEX
Query on OEX

A1, A2, a1, a2 CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B1, C1, C2, a1, a2, b1, c1, c2, i1 GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCT
Query on BCT

A1, A2, a1, a2 BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A1, A2, a1, a2 FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

O1, o2 CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A1, A2, a1, a2 CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNL
Query on UNL

Unknown ligand
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 0.278
  • R-Value Work: 0.249
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 210.45 α = 90.00
b = 240.31 β = 90.00
c = 300.06 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2015-03-19
  • Released Date: 2016-01-20
  • Deposition author(s): Ago, H., Shen, J.-R.

Revision History

  • 2016-02-03
    Type: Database references
  • 2016-03-23
    Type: Database references