4WD2 | pdb_00004wd2

Crystal structure of an aromatic amino acid aminotransferase from Burkholderia cenocepacia J2315

• PDB DOI: https://doi.org/10.2210/pdb4WD2/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia cenocepacia K56-2Valvano
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-09-06 Released: 2014-10-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.151 (Depositor), 0.152 (DCC) 
• R-Value Work: 
  0.116 (Depositor), 0.115 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of an aromatic amino acid aminotransferase from Burkholderia cenocepacia J2315

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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: 45.26 kDa 
• Atom Count: 3,456 
• Modeled Residue Count: 398 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic-amino-acid transaminase TyrB	A	408	Burkholderia cenocepacia K56-2Valvano	Mutation(s): 0  Gene Names: tyrB, BURCENK562V_C3553 EC: 2.6.1.57

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A], C [auth A], D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.151 (Depositor), 0.152 (DCC) 
• R-Value Work:  0.116 (Depositor), 0.115 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34WD2

Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.22	α = 90
b = 59.22	β = 90
c = 200.27	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 2.0: 2017-11-22
  Changes: Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2023-11-15
  Changes: Data collection, Database references