1WDD

Crystal Structure of Activated Rice Rubisco Complexed with 2-Carboxyarabinitol-1,5-bisphosphate

Structural Biology Knowledgebase: 1WDD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182
  • R-Value Work: 0.160

Literature

Macromolecules
Sequence Display for 1WDD

Classification: LYASE

Total Structure Weight: 138274.50

Macromolecule Entities
Molecule Chains Length Organism Details
Ribulose bisphosphate carboxylase large chain A, E 477 Oryza sativa EC#: 4.1.1.39 IUBMB
Gene Name(s): rbcL LOC_Osp1g00420 Nip064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribulose bisphosphate carboxylase small chain C S, W 128 Oryza sativa EC#: 4.1.1.39 IUBMB
Gene Name(s): RBCS RBCS-C Os12g0274700 LOC_Os12g17600 OsJ_016909
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A, E, W GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, E 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, E L-PEPTIDE LINKING C7 H14 N2 O4 LYS
MME
Query on MME
S, W L-PEPTIDE LINKING C6 H13 N O2 S MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182
  • R-Value Work: 0.160
  • Space Group: I 4
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 111.71 α = 90.00
b = 111.71 β = 90.00
c = 196.78 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-13
  • Released Date: 2004-11-13
  • Deposition author(s): Mizohata, E., Matsumura, H., Ueno, T., Ishida, H., Inoue, T., Makino, A., Mae, T., Kai, Y.

Revision History

  • 2013-06-05
    Type: Citation | Details: Citation update
  • 2012-06-13
    Type: Citation | Details: Citation update
  • 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