2AFR

The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis

• PDB DOI: https://doi.org/10.2210/pdb2AFR/pdb

• Classification: ISOMERASE
• Organism(s): Leptospira interrogans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-07-26 Released: 2006-04-04 
• Deposition Author(s): Xue, Y., Wei, Z., Li, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

The crystal structure of putative precorrin isomerase CbiC in cobalamin biosynthesis

Xue, Y., Wei, Z., Li, X., Gong, W.

(2006) J Struct Biol 153: 307-311

• PubMed: 16427313 
• DOI: https://doi.org/10.1016/j.jsb.2005.11.011
• Primary Citation of Related Structures:  
  2AFR, 2AFV


• PubMed Abstract: 
  

  The leptospira cbiC encodes the enzyme catalyzing the methyl rearrangement reaction of the cobalamin biosynthesis pathway. The protein has been cloned and overexpressed as a His-tagged recombinant protein in Escherichia coli. The crystal structures have been solved in two crystal forms (P4(2)2(1)2 and P3(1)21) diffracting to 3.0 and 2.3A resolution, respectively. The structures are similar to the precorrin-8x methyl mutase (CobH), an enzyme of the aerobic pathway to vitamin B12.

---

Organizational Affiliation: 

National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, PR China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 25.89 kDa 
• Atom Count: 1,729 
• Modelled Residue Count: 216 
• Deposited Residue Count: 231 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cobalamin biosynthesis precorrin isomerase	A	231	Leptospira interrogans	Mutation(s): 0  EC: 5.4.1.2 (PDB Primary Data), 5.4.99.60 (UniProt)
UniProt
Find proteins for Q8EXP7 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)) Explore Q8EXP7  Go to UniProtKB:  Q8EXP7

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.284 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.885	α = 90
b = 55.885	β = 90
c = 142.551	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-04 
Deposition Author(s): Xue, Y., Wei, Z., Li, X.

Revision History  

• Version 1.0: 2006-04-04
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references