1JB0

Crystal Structure of Photosystem I: a Photosynthetic Reaction Center and Core Antenna System from Cyanobacteria

Structural Biology Knowledgebase: 1JB0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1JB0

Classification: PHOTOSYNTHESIS

Total Structure Weight: 359704.03

Macromolecule Entities
Molecule Chains Length Organism Details
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A1 A 755 Synechococcus elongatus EC#: 1.1.1.239 IUBMB 1.97.1.12 IUBMB
Gene Name(s): psaA tlr0731
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM I P700 CHLOROPHYLL A APOPROTEIN A2 B 740 Synechococcus elongatus EC#: 1.97.1.12 IUBMB
Gene Name(s): psaB tlr0732
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM I IRON-SULFUR CENTER C 80 Synechococcus elongatus EC#: 1.97.1.12 IUBMB
Gene Name(s): psaC tsl1013
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT II D 138 Synechococcus elongatus Gene Name(s): psaD tll1724
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IV E 75 Synechococcus elongatus Gene Name(s): psaE tsl1567
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT III F 164 Synechococcus elongatus Gene Name(s): psaF tlr2411
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT VIII I 38 Synechococcus elongatus Gene Name(s): psaI tsr2405
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT IX J 41 Synechococcus elongatus Gene Name(s): psaJ tsr2412
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT X K 83 Synechococcus elongatus Gene Name(s): psaK tsr2273
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XI L 154 Synechococcus elongatus Mutation: P46R
Gene Name(s): psaL tlr2404
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM 1 REACTION CENTRE SUBUNIT XII M 31 Synechococcus elongatus Gene Name(s): psaM tsr0197
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
PHOTOSYSTEM I SUBUNIT PSAX X 35 Synechococcus elongatus Gene Name(s): tsr0813
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Photosystems

Protein Name: Photosystem I


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

A, B, F, J, K, L, M, X 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)
LHG
Query on LHG

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

A, B, F, I, J, L, M BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-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

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

L CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.199
  • Space Group: P 63

Unit Cell:

Length (Å) Angle (°)
a = 281.00 α = 90.00
b = 281.00 β = 90.00
c = 165.20 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-01
  • Released Date: 2001-08-01
  • Deposition author(s): Jordan, P., Fromme, P., Witt, H.T., Klukas, O., Saenger, W., Krauss, N.

Revision History

  • 2016-05-11
    Type: Biological assembly | Details: corrected biological assembly
  • 2012-07-25
    Type: Non-polymer description | Details: Change CLA residue to CL1
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4