2VDH

CRYSTAL STRUCTURE OF CHLAMYDOMONAS REINHARDTII RUBISCO WITH A LARGE-SUBUNIT C172S MUTATION

Structural Biology Knowledgebase: 2VDH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.171

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VDH

Classification: LYASE

Total Structure Weight: 558302.85

Macromolecule Entities
Molecule Chains Length Organism Details
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 475 Chlamydomonas reinhardtii EC#: 4.1.1.39 IUBMB
Mutation: L46P, C172S
Gene Name(s): rbcL
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN 1 I, J, K..., L, M, N, O, PI, J, K, L, M, N, O, P 140 Chlamydomonas reinhardtii EC#: 4.1.1.39 IUBMB
Gene Name(s): RBCS-1

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 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer
 
JSmol
EDO
Query on EDO

A, B, C, D, E, F, G, H, I, J, K, L, M, N, O 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
MG
Query on MG

A, B, C, D, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
Modified Residues 4 Unique
ID Chains Type Formula 2D Diagram Parent
HYP
Query on HYP
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C5 H9 N O3 PRO
KCX
Query on KCX
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C7 H14 N2 O4 LYS
SMC
Query on SMC
A, B, C, D, E, F, G, H L-PEPTIDE LINKING C4 H9 N O2 S CYS
MME
Query on MME
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: 2.3 Å
  • R-Value Free: 0.203
  • R-Value Work: 0.171
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 120.19 α = 90.00
b = 178.35 β = 117.87
c = 122.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-10-09
  • Released Date: 2008-11-04
  • Deposition author(s): Garcia-Murria, M.-J., Karkehabadi, S., Marin-Navarro, J., Satagopan, S., Andersson, I., Spreitzer, R.J., Moreno, J.

Revision History

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