2V63

Crystal structure of Rubisco from Chlamydomonas reinhardtii with a large-subunit V331A mutation

Structural Biology Knowledgebase: 2V63 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.191

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2V63

Classification: OXIDOREDUCTASE

Total Structure Weight: 557524.44

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, V331A
Gene Name(s): rbcL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
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
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, B, C, D, E, F, G, H 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
C6 H14 O13 P2
ITHCSGCUQDMYAI-ZMIZWQJLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

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

A, B, C, D, E, F, G, H 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 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: 1.8 Å
  • R-Value Free: 0.214
  • R-Value Work: 0.191
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 121.38 α = 90.00
b = 177.45 β = 117.65
c = 122.57 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-07-13
  • Released Date: 2007-07-31
  • Deposition author(s): Karkehabadi, S., Satagopagan, S., Taylor, T.C., Spreitzer, R.J., Andersson, I.

Revision History

  • 2015-02-04
    Type: Linkage | Details: CONECT
  • 2015-02-04
    Type: Version format compliance | Details: REMARK 4
  • 2015-02-04
    Type: Polymer description | Details: COMPND
  • 2015-02-04
    Type: Entry authorship | Details: AUTHOR
  • 2015-02-04
    Type: Citation | Details: JRNL
  • 2015-02-04
    Type: Other | Details: TER,REMARK 525,MASTER,REMARK 280
  • 2015-02-04
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2015-02-04
    Type: Geometry validation | Details: REMARK 500
  • 2015-02-04
    Type: Function and keywords | Details: KEYWDS
  • 2015-02-04
    Type: Secondary structure | Details: HELIX
  • 2015-02-04
    Type: Sequence database correspondence | Details: SEQADV
  • 2015-02-04
    Type: Atom nomenclature | Details: ATOM,HETATM