6CFQ | pdb_00006cfq

Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei with INH bound

PDB DOI: https://doi.org/10.2210/pdb6CFQ/pdb

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

Deposited: 2018-02-16 Released: 2018-02-28
Deposition Author(s): Loewen, P.C.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canada Research Chair Program

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.170 (Depositor), 0.180 (DCC)
R-Value Work:
0.141 (Depositor), 0.160 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei with INH bound

Loewen, P.C.

To be published.

Macromolecule Content

Total Structure Weight: 161.35 kDa
Atom Count: 12,876
Modeled Residue Count: 1,426
Deposited Residue Count: 1,456
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catalase-peroxidase	A, B	728	Burkholderia pseudomallei	Mutation(s): 1 Gene Names: katG, BOC41_00140, BOC42_10690, DP46_2227, DP49_6664 EC: 1.11.1.21
UniProt
Find proteins for Q939D2 (Burkholderia pseudomallei (strain K96243)) Explore Q939D2 Go to UniProtKB: Q939D2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q939D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A], K [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
NIZ Query on NIZ Download Ideal Coordinates CCD File SDF format, chain S [auth B] MOL2 format, chain S [auth B] mmCIF format, chain S [auth B]	S [auth B]	pyridine-4-carbohydrazide C₆ H₇ N₃ O QRXWMOHMRWLFEY-UHFFFAOYSA-N		Interactions Focus chain S [auth B] Interactions & Density Focus chain S [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], P [auth B], R [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain R [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain P [auth B] Focus chain R [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain G [auth A] MOL2 format, chain O [auth B] MOL2 format, chain G [auth A] mmCIF format, chain O [auth B] mmCIF format, chain G [auth A]	G [auth A], O [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A]	E [auth A], M [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain M [auth B] Interactions & Density Focus chain E [auth A] Focus chain M [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain N [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	F [auth A], J [auth A], N [auth B], Q [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain Q [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A]	D [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.170 (Depositor), 0.180 (DCC)
R-Value Work: 0.141 (Depositor), 0.160 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.641	α = 90
b = 115.506	β = 90
c = 174.546	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Loewen, P.C.

Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	D9600_2012
Canada Research Chair Program	Canada	--

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary