3D64 | pdb_00003d64

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3D64/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-18 Released: 2008-06-03 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Burkholderia pseudomallei.

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.44 kDa 
• Atom Count: 7,992 
• Modeled Residue Count: 924 
• Deposited Residue Count: 988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenosylhomocysteinase	A, B	494	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: ahcY, BURPS1710b_0057 EC: 3.3.1.1 (PDB Primary Data), 3.13.2.1 (UniProt)
UniProt
Find proteins for Q3JY79 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JY79  Go to UniProtKB:  Q3JY79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	C [auth A], D [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.363	α = 90
b = 186.363	β = 90
c = 104.403	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Refinement description