4PBC | pdb_00004pbc

X-ray crystal structure of a putative D-amino acid aminotransferase from Burkholderia cenocepacia

• PDB DOI: https://doi.org/10.2210/pdb4PBC/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia cenocepacia J2315
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-12 Released: 2014-07-02 
• Deposition Author(s): Fairman, J.W., Abendroth, J., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

X-ray crystal structure of a putative D-amino acid aminotransferase from Burkholderia cenocepacia

Fairman, J.W., Abendroth, J., Edwards, T.E., Lorimer, D.

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 (software)

Macromolecule Content 

• Total Structure Weight: 70.57 kDa 
• Atom Count: 4,766 
• Modeled Residue Count: 575 
• Deposited Residue Count: 632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-amino acid aminotransferase	A, B	316	Burkholderia cenocepacia J2315	Mutation(s): 0  Gene Names: BCAL0705
UniProt
Find proteins for B4E9Q5 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4E9Q5  Go to UniProtKB:  B4E9Q5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34PBC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.08	α = 90
b = 102.97	β = 90
c = 152.22	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-02 
Deposition Author(s): Fairman, J.W., Abendroth, J., Edwards, T.E., Lorimer, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2014-07-02
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.2: 2017-11-22
  Changes: Refinement description
• Version 1.3: 2019-12-11
  Changes: Author supporting evidence
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Refinement description