5TQI | pdb_00005tqi

Crystal structure of a pyridoxal kinase from Burkholderia multivorans

• PDB DOI: https://doi.org/10.2210/pdb5TQI/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia multivorans ATCC 17616
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-24 Released: 2016-11-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Literature

Crystal structure of a pyridoxal kinase from Burkholderia multivorans

Levin, E.J., Abendroth, J., Lorimer, D.D., Edwards, T.E.

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: 64.55 kDa 
• Atom Count: 5,170 
• Modeled Residue Count: 575 
• Deposited Residue Count: 588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal kinase PdxY	A, B	294	Burkholderia multivorans ATCC 17616	Mutation(s): 0  Gene Names: pdxK, pdxY, BMULJ_01107 EC: 2.7.1.35
UniProt
Find proteins for A0A0H3KDL9 (Burkholderia multivorans (strain ATCC 17616 / 249)) Explore A0A0H3KDL9  Go to UniProtKB:  A0A0H3KDL9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A], D [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35TQI

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.97	α = 90
b = 42.49	β = 115.56
c = 90.51	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references