2WSE

Improved Model of Plant Photosystem I

Structural Biology Knowledgebase: 2WSE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.375
  • R-Value Work: 0.369

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2WSE

Classification: PHOTOSYNTHESIS

Total Structure Weight: 651648.35

Macromolecule Entities
Molecule Chains Length Organism Details
AT3G54890 1 241 Arabidopsis thaliana EC#: 2.7.7.n6 IUBMB
Mutation: K-33I, K-1R
Gene Name(s): LHCA1 CAB6 At3g54890 F28P10.130
TYPE II CHLOROPHYLL A/B BINDING PROTEIN FROM PHOTOSYSTEM I 2 269 Pisum sativum Mutation: ΔG258
Gene Name(s): lhaB
LHCA3 3 276 Glycine max Gene Name(s):
CHLOROPHYLL A-B BINDING PROTEIN P4, CHLOROPLASTIC 4 251 Pisum sativum Mutation: ΔA211
Gene Name(s): lhcA-P4
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 A 758 Pisum sativum EC#: 1.97.1.12 IUBMB
Gene Name(s): psaA psaA1
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 B 734 Pisum sativum EC#: 1.97.1.12 IUBMB
Gene Name(s): psaB psaA2
PHOTOSYSTEM I IRON-SULFUR CENTER C 81 Pisum sativum EC#: 1.97.1.12 IUBMB
Gene Name(s): psaC frxA
PHOTOSYSTEM I REACTION CENTER SUBUNIT II, CHLOROPLASTIC D 212 Spinacia oleracea Mutation: A-52G, Q-50P, P-44R, D-34E, H-11L, S-9T, P12T, G14A
Gene Name(s): psaD
PHOTOSYSTEM I REACTION CENTER SUBUNIT IV A, CHLOROPLASTIC E 143 Arabidopsis thaliana Gene Name(s): PSAE1 At4g28750 F16A16.140
PHOTOSYSTEM I REACTION CENTER SUBUNIT III, CHLOROPLASTIC F 231 Spinacia oleracea Gene Name(s): PSAF
PHOTOSYSTEM I REACTION CENTER SUBUNIT V, CHLOROPLASTIC G 167 Spinacia oleracea Gene Name(s): PSAG
PHOTOSYSTEM I REACTION CENTER SUBUNIT VI, CHLOROPLASTIC H 144 Spinacia oleracea Gene Name(s): PSAH
PHOTOSYSTEM I REACTION CENTER SUBUNIT VIII I 40 Pisum sativum Gene Name(s): psaI
PHOTOSYSTEM I REACTION CENTER SUBUNIT IX J 44 Spinacia oleracea Gene Name(s): psaJ
PHOTOSYSTEM I REACTION CENTER SUBUNIT PSAK, CHLOROPLASTIC K 131 Hordeum vulgare Mutation: L47I
Gene Name(s): PSAK
PHOTOSYSTEM I REACTION CENTER SUBUNIT XI, CHLOROPLASTIC L 216 Spinacia oleracea Gene Name(s): PSAL
PHOTOSYSTEM I-N SUBUNIT N 170 Phaseolus vulgaris Gene Name(s): PSI-N PHAVU_002G269400g
PHOTOSYSTEM I-N SUBUNIT R 53 Pisum sativum

Membrane Protein

Source: inferred by homology | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem I (plant)


Small Molecules
Ligands 8 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLA
Query on CLA

1, 2, 3, 4, A, B, F, G, I, J, K, L, R CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMG
Query on LMG

B 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BCR
Query on BCR

3, A, B, I, L BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
LMU
Query on LMU

1, 2, 4, A, B, K, L, N, R DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PQN
Query on PQN

A, B PHYLLOQUINONE
4-NAPHTHOQUINONE, (Synonym)
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

B, C IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SUC
Query on SUC

2, 3, B, F SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
UNL
Query on UNL

Unknown ligand
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
UNK
Query on UNK
R L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.49 Å
  • R-Value Free: 0.375
  • R-Value Work: 0.369
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 120.65 α = 90.00
b = 189.09 β = 91.24
c = 129.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-05
  • Released Date: 2009-11-17
  • Deposition author(s): Amunts, A., Toporik, H., Borovikov, A., Nelson, N.

Revision History

  • 2012-08-08
    Type: Biological assembly | Details: REMARK 350
  • 2012-08-08
    Type: Linkage | Details: CONECT,LINK
  • 2012-08-08
    Type: Polymer description | Details: COMPND
  • 2012-08-08
    Type: Citation | Details: JRNL
  • 2012-08-08
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2012-08-08
    Type: Non-polymer description | Details: FORMUL,REMARK 620,HETNAM,HET
  • 2012-08-08
    Type: Geometry validation | Details: REMARK 500
  • 2012-08-08
    Type: Version format compliance | Details: REMARK 4
  • 2012-08-08
    Type: Function and keywords | Details: KEYWDS
  • 2012-08-08
    Type: Other | Details: REMARK 610,MASTER
  • 2012-08-08
    Type: Atom nomenclature | Details: HETATM