5KSG

Crystal structure of the W153F variant of catalase-peroxidase from B. pseudomallei treated with isoniazid

• PDB DOI: https://doi.org/10.2210/pdb5KSG/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-07-08 Released: 2017-07-12 
• Deposition Author(s): Loewen, P.C.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.159 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 

Starting Model: experimental

Literature

Structure of the W153 variant of catalase-peroxidase of B. pseudomallei at 1.62 Angstroms.

Loewen, P.C.

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: 161.27 kDa 
• Atom Count: 12,995 
• Modelled Residue Count: 1,427 
• Deposited Residue Count: 1,456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B	728	Burkholderia pseudomallei 1710b	Mutation(s): 1  Gene Names: katG, BURPS1710b_3366 EC: 1.11.1.21
UniProt
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JNW6  Go to UniProtKB:  Q3JNW6

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NIZ	S [auth B]	pyridine-4-carbohydrazide C6 H7 N3 O QRXWMOHMRWLFEY-UHFFFAOYSA-N
MPD	I [auth A], J [auth A], Q [auth B], R [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	H [auth A], P [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL	E [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY	F [auth A], G [auth A], N [auth B], O [auth B]	OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N
NA	D [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.159 
• R-Value Work: 0.135 
• R-Value Observed: 0.136 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.665	α = 90
b = 115.928	β = 90
c = 174.349	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-07-12 
Deposition Author(s): Loewen, P.C.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	D9600

Revision History  

• Version 1.0: 2017-07-12
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary