1IR1

Crystal Structure of Spinach Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco) Complexed with CO2, Mg2+ and 2-Carboxyarabinitol-1,5-Bisphosphate

Structural Biology Knowledgebase: 1IR1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.155

Literature

Macromolecules
Sequence Display for 1IR1

Classification: LYASE

Total Structure Weight: 271674.34

Macromolecule Entities
Molecule Chains Length Organism Details
Large subunit of Rubisco A, B, C, D 475 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Mutation: K201X
Gene Name(s): rbcL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Small subunit of Rubisco S, T, U, V 123 Spinacia oleracea EC#: 4.1.1.39 IUBMB
Mutation: M1X
Gene Name(s): RBCS2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B, C, D L-PEPTIDE LINKING C7 H14 N2 O4 LYS
MME
Query on MME
S, T, U, V L-PEPTIDE LINKING C6 H13 N O2 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.179
  • R-Value Work: 0.155
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 157.80 α = 90.00
b = 157.80 β = 90.00
c = 200.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-08-31
  • Released Date: 2002-03-13
  • Deposition author(s): Mizohata, E., Matsumura, H., Okano, Y., Kumei, M., Takuma, H., Onodera, J., Kato, K., Shibata, N., Inoue, T., Yokota, A., Kai, Y.
  • Previous versions: 1BUR

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values