5KSG

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


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
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

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

Loewen, P.C.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase-peroxidase
A, B
728Burkholderia pseudomallei 1710bMutation(s): 1 
Gene Names: katGBURPS1710b_3366
EC: 1.11.1.21
UniProt
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JNW6 
Go to UniProtKB:  Q3JNW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JNW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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C [auth A],
K [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NIZ
Query on NIZ

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S [auth B]pyridine-4-carbohydrazide
C6 H7 N3 O
QRXWMOHMRWLFEY-UHFFFAOYSA-N
MPD
Query on MPD

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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
Query on PO4

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H [auth A],
P [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

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E [auth A],
M [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
OXY
Query on OXY

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F [auth A],
G [auth A],
N [auth B],
O [auth B]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
NA
Query on NA

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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 = 100.665α = 90
b = 115.928β = 90
c = 174.349γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

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

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaD9600

Revision History  (Full details and data files)

  • 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