3KDN

Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP

Structural Biology Knowledgebase: 3KDN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.213

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3KDN

Classification: LYASE

Total Structure Weight: 502295.21

Macromolecule Entities
Molecule Chains Length Organism Details
Ribulose bisphosphate carboxylase A, B, C..., D, E, F, G, H, I, JA, B, C, D, E, F, G, H, I, J 444 Thermococcus kodakarensis EC#: 4.1.1.39 IUBMB
Mutation: G326E, K327R, W328D, D329I, V330T
Gene Name(s): rbcL rbc TK2290

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

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

A, B, C, D, E, F, G, H, I, J MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
KCX
Query on KCX
A, B, C, D, E, F, G, H, I, J L-PEPTIDE LINKING C7 H14 N2 O4 LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.213
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.47 α = 90.00
b = 246.24 β = 104.10
c = 133.08 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-10-23
  • Released Date: 2010-10-06
  • Deposition author(s): Nishitani, Y., Fujihashi, M., Doi, T., Yoshida, S., Atomi, H., Imanaka, T., Miki, K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4