2AXT

Crystal Structure of Photosystem II from Thermosynechococcus elongatus

Structural Biology Knowledgebase: 2AXT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.234

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2AXT

Classification: ELECTRON TRANSPORT

Total Structure Weight: 717578.38

Macromolecule Entities
Molecule Chains Length Organism Details
Photosystem Q(B) protein A, a 344 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Fragment: residues 1-344
Gene Name(s): psbA1 psbA-1 tlr1843
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
CP47 protein B, b 510 Thermosynechococcus elongatus Gene Name(s): psbB tlr1530
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
photosystem II CP43 protein C, c 473 Thermosynechococcus elongatus Gene Name(s): psbC tlr1631
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
photosystem II reaction center D2 protein D, d 352 Thermosynechococcus elongatus EC#: 1.10.3.9 IUBMB
Gene Name(s): psbD1 tlr0455 psbD2 tlr1630
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 alpha subunit E, e 84 Thermosynechococcus elongatus Gene Name(s): psbE tsr1541
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome b559 beta subunit F, f 45 Thermosynechococcus elongatus Gene Name(s): psbF tsr1542
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center H protein H, h 66 Thermosynechococcus elongatus Gene Name(s): psbH tsl1386
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center I protein I, i 38 Thermosynechococcus elongatus Gene Name(s): psbI tsr1074
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center J protein J, j 40 Thermosynechococcus elongatus Gene Name(s): psbJ tsr1544
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center protein K K, k 37 Thermosynechococcus elongatus Gene Name(s): psbK tsl0176
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center L protein L, l 37 Thermosynechococcus elongatus Gene Name(s): psbL tsr1543
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center M protein M, m 36 Thermosynechococcus elongatus Gene Name(s): psbM tsl2052
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II manganese-stabilizing polypeptide O, o 247 Thermosynechococcus elongatus Gene Name(s): psbO tll0444
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II reaction center T protein T, t 32 Thermosynechococcus elongatus Gene Name(s): psbT tsr1531
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Photosystem II 12 kDa extrinsic protein U, u 104 Thermosynechococcus elongatus Gene Name(s): psbU tll2409
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Cytochrome c-550 V, v 137 Thermosynechococcus elongatus Gene Name(s): psbV tll1285
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Unassigned subunits X, x 129 Thermosynechococcus elongatus
Photosystem II reaction center Z protein Z, z 62 Thermosynechococcus elongatus Gene Name(s): psbZ tsr1967
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem II


Small Molecules
Ligands 15 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DGD
Query on DGD

C, H, c, h DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
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, a PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SQD
Query on SQD

A, L, a, d, t 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LHG
Query on LHG

A, a 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MGE
Query on MGE

B, D, I, L, b, d, i, l (1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL PALMITATE
MONOGALACTOSYL-DIACYLGLYCEROL (Synonym)
C38 H72 O10
FIJGNIAJTZSERN-DQQGJSMTSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
HEM
Query on HEM

F, V, f, v PROTOPORPHYRIN IX CONTAINING FE
HEME (Synonym)
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PQ9
Query on PQ9

A, D, a, d 5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27- HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]- 2,3-DIMETHYLBENZO-1,4-QUINONE
C43 H64 O2
JXUCGUASMMLSBH-HOHOQCMASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

A, B, C, D, H, T, X, a, b, c, d, h, t, x BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMT
Query on LMT

A, M, T, a, m, t 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)
UNK
Query on UNK

C, X, c, x UNKNOWN
C4 H9 N O2
QWCKQJZIFLGMSD-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCT
Query on BCT

D, d BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE2
Query on FE2

A, a FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

K, k CALCIUM ION
Ca
BHPQYMZQTOCNFJ-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
C, X, c, x L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.286
  • R-Value Work: 0.234
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 127.69 α = 90.00
b = 225.40 β = 90.00
c = 306.11 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-09-06
  • Released Date: 2005-12-27
  • Deposition author(s): Loll, B., Kern, J., Saenger, W., Zouni, A., Biesiadka, J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name