3KE5 | pdb_00003ke5

Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus in a complex with ATP

• PDB DOI: https://doi.org/10.2210/pdb3KE5/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus cereus ATCC 14579
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-23 Released: 2010-10-20 
• Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.225 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.197 (DCC) 

Starting Model: experimental

Literature

Crystal structure of a PduO-Type ATP:Cob(I)alamin adenosyltransferase from Bacillus cereus in a complex with ATP

Park, A.K., Moon, J.H., Chi, Y.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 73.4 kDa 
• Atom Count: 4,705 
• Modeled Residue Count: 540 
• Deposited Residue Count: 639 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical Cytosolic Protein	A, B, C	213	Bacillus cereus ATCC 14579	Mutation(s): 0  EC: 2.5.1.17
UniProt
Find proteins for Q813T7 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q813T7  Go to UniProtKB:  Q813T7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A], F [auth B], H [auth C]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
MG	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.225 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.197 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.925	α = 90
b = 137.042	β = 90
c = 158.263	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-20 
Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

Revision History  

• Version 1.0: 2010-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description