2AFV

The Crystal Structure of Putative Precorrin Isomerase CbiC in Cobalamin Biosynthesis

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1016/j.jsb.2005.11.011

  • 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.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cobalamin biosynthesis precorrin isomerase
A, B
231Leptospira interrogansMutation(s): 0 
EC: 5.4.1.2
UniProt
Find proteins for Q8EXP7 (Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601))
Explore Q8EXP7 
Go to UniProtKB:  Q8EXP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EXP7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P33
Query on P33
Download Ideal Coordinates CCD File 
L [auth B]3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
C14 H30 O8
XPJRQAIZZQMSCM-UHFFFAOYSA-N
P6G
Query on P6G
Download Ideal Coordinates CCD File 
G [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.078α = 90
b = 113.078β = 90
c = 114.502γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations, Structure summary