2ZHZ

Crystal structure of a pduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis

• PDB DOI: https://doi.org/10.2210/pdb2ZHZ/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia thailandensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-02-12 Released: 2008-07-29 
• Deposition Author(s): Moon, J.H., Park, A.K., Jang, E.H., Kim, H.S., Chi, Y.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.211 

Literature

Crystal structure of a PduO-type ATP:cobalamin adenosyltransferase from Burkholderia thailandensis.

Moon, J.H., Park, A.K., Jang, E.H., Kim, H.S., Chi, Y.M.

(2008) Proteins 72: 1066-1070

• PubMed: 18473361 
• DOI: https://doi.org/10.1002/prot.22084
• Primary Citation of Related Structures:  
  2ZHY, 2ZHZ

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Organizational Affiliation: 

Institute of Life Science and Natural Resources, Korea University, Seoul 136-713, Korea.

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: 59.91 kDa 
• Atom Count: 4,038 
• Modelled Residue Count: 494 
• Deposited Residue Count: 549 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP:cob(I)alamin adenosyltransferase, putative	A, B, C	183	Burkholderia thailandensis	Mutation(s): 0  Gene Names: pduO EC: 2.5.1.17 (PDB Primary Data), 2.5.1 (UniProt)
UniProt
Find proteins for Q2SZ09 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2SZ09  Go to UniProtKB:  Q2SZ09

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	G [auth B], H [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GOL	E [auth A], I [auth B], J [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.211 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.907	α = 90
b = 148.174	β = 90
c = 158.096	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-29 
Deposition Author(s): Moon, J.H., Park, A.K., Jang, E.H., Kim, H.S., Chi, Y.M.

Revision History  

• Version 1.0: 2008-07-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations