1IR2

Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP)

Structural Biology Knowledgebase: 1IR2 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.152

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1IR2

Classification: LYASE

Total Structure Weight: 1113903.28

Macromolecule Entities
Molecule Chains Length Organism Details
Large subunit of Rubisco A, B, C..., D, E, F, G, H, S, T, U, V, W, X, Y, ZA, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z 475 Chlamydomonas reinhardtii EC#: 4.1.1.39 IUBMB
Mutation: L46P, P104X, P151X, K201X, C256X, C369X
Gene Name(s): rbcL
Small subunit of Rubisco 1, 2, 3..., 4, 5, 6, 7, 8, I, J, K, L, M, N, O, P1, 2, 3, 4, 5, 6, 7, 8, I, J, K, L, M, N, O, P 140 Chlamydomonas reinhardtii EC#: 4.1.1.39 IUBMB
Mutation: M1X
Gene Name(s): RBCS-2

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

A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 4 Unique
ID Chains Type Formula 2D Diagram Parent
HYP
Query on HYP
A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z L-PEPTIDE LINKING C5 H9 N O3 PRO
KCX
Query on KCX
A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z L-PEPTIDE LINKING C7 H14 N2 O4 LYS
SMC
Query on SMC
A, B, C, D, E, F, G, H, S, T, U, V, W, X, Y, Z L-PEPTIDE LINKING C4 H9 N O2 S CYS
MME
Query on MME
1, 2, 3, 4, 5, 6, 7, 8, I, J, K, L, M, N, O, P L-PEPTIDE LINKING C6 H13 N O2 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.181
  • R-Value Work: 0.152
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 129.17 α = 90.00
b = 174.75 β = 97.75
c = 222.27 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-03
  • Released Date: 2002-03-20
  • 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.

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