2CBF | pdb_00002cbf

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF

• PDB DOI: https://doi.org/10.2210/pdb2CBF/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.281 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.181 (DCC) 

Starting Model: experimental

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 Biol 5: 585-592

• PubMed: 9665173 
• DOI: https://doi.org/10.1038/846
• Primary Citation Related Structures: 
  1CBF, 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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Organizational Affiliation: 
• Department of Chemistry, University of York, Heslington, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 25.89 kDa 
• Atom Count: 1,807 
• Modeled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
COBALT-PRECORRIN-4 TRANSMETHYLASE	A	234	Priestia megaterium	Mutation(s): 0  Gene Names: CBIF EC: 2.1.1.133 (PDB Primary Data), 2.1.1.271 (UniProt)
UniProt
Find proteins for O87696 (Priestia megaterium) Explore O87696  Go to UniProtKB:  O87696

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	B [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.281 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.181 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.04	α = 90
b = 80.04	β = 90
c = 77.96	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 1999-05-11
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description