Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 31570.40 
• Atom Count: 1858 
• Residue Count: 285 
• Unique protein chains: 1

1CBF

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF

• DOI: 10.2210/pdb1CBF/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Bacillus megaterium
• Expression System: Escherichia coli


• Deposited: 1998-05-01 Released: 1999-05-11 
• Deposition Author(s): Schubert, H.L., Raux, E., Woodcock, S.C., Wilson, K.S., Warren, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.195 

Literature

The X-ray structure of a cobalamin biosynthetic enzyme, cobalt-precorrin-4 methyltransferase.

Schubert, H.L., Wilson, K.S., Raux, E., Woodcock, S.C., Warren, M.J.

(1998) Nat.Struct.Mol.Biol. 5: 585-592

• PubMed: 9665173 
• DOI: 10.1038/846
• Primary Citation of Related Structures:  
  2CBF


• PubMed Abstract: 
  

Biosynthesis of the corrin ring of vitamin B12 requires the action of six S-adenosyl-L-methionine (AdoMet) dependent transmethylases, closely related in sequence. The first X-ray structure of one of these, cobalt-precorrin-4 transmethylase, CbiF, from Bacillus megaterium has been determined to a resolution of 2.4 A. CbiF contains two alphabeta domains forming a trough in which S-adenosyl-L-homocysteine (AdoHcy) binds. The location of AdoHcy and a number of conserved residues, helps define the precorrin binding site. A second crystal form determined at 3.1 A resolution highlights the flexibility of two loops around this site. CbiF employs a unique mode of AdoHcy binding and represents a new class of transmethylase.

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Related Citations: 

• Cobalamin (Vitamin B12) Biosynthesis--Cloning, Expression and Crystallisation of the Bacillus Megaterium S-Adenosyl-L-Methionine-Dependent Cobalt-Precorrin-4 Transmethylase Cbif
  Raux, E.,Schubert, H.L.,Woodcock, S.C.,Wilson, K.S.,Warren, M.J.
  (1998) Eur.J.Biochem. 254: 341




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Organizational Affiliation: 

Department of Chemistry, University of York, Heslington, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
COBALT-PRECORRIN-4 TRANSMETHYLASE	A	285	Bacillus megaterium	Mutation(s): 0  Gene Names: cbiF EC: 2.1.1.271
Find proteins for O87696 (Bacillus megaterium) Go to UniProtKB:  O87696

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
SAH	A	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Free: 0.247 
• R-Value Work: 0.195 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 80.700	α = 90.00
b = 80.700	β = 90.00
c = 109.400	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
MLPHARE	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-01 
• Released Date: 1999-05-11 
• Deposition Author(s): Schubert, H.L., Raux, E., Woodcock, S.C., Wilson, K.S., Warren, M.J.

Revision History 

• Version 1.0: 1999-05-11
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Derived calculations, Version format compliance