2BB3

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb2BB3/pdb

• Classification: TRANSFERASE
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-10-17 Released: 2005-11-29 
• Deposition Author(s): Kim, Y., Joachimiak, A., Xu, X., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.274 (Depositor), 0.266 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal Structure of Cobalamin Biosynthesis Precorrin-6Y Methylase (cbiE) from Archaeoglobus fulgidus

Kim, Y., Xu, X., Savchenko, A., Edwards, A., Joachimiak, A.

To be published.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 51.27 kDa 
• Atom Count: 3,503 
• Modelled Residue Count: 386 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
cobalamin biosynthesis precorrin-6Y methylase (cbiE)	A, B	221	Archaeoglobus fulgidus DSM 4304	Mutation(s): 5  EC: 2.1.1
UniProt
Find proteins for O29536 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29536  Go to UniProtKB:  O29536

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.274 (Depositor), 0.266 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.191	α = 90
b = 88.418	β = 90
c = 115.932	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-29 
Deposition Author(s): Kim, Y., Joachimiak, A., Xu, X., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2005-11-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary