Download MendeleyCrystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei
Loewen, P.C.To be published.
6CEK | pdb_00006cek
Crystal structure of the D141N variant of catalase-peroxidase from B. pseudomallei
- PDB DOI: https://doi.org/10.2210/pdb6CEK/pdb
- Classification: OXIDOREDUCTASE
- Organism(s): Burkholderia pseudomallei 1710b
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2018-02-12 Released: 2018-02-21
- Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canada Research Chair Program
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.173 (Depositor), 0.180 (DCC)
- R-Value Work: 0.147 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.148 (Depositor)
Starting Model: experimental
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This is version 1.3 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Catalase-peroxidase | 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 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q3JNW6 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| HEM Query on HEM | C [auth A], K [auth B] | PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L |  | ||
| MPD Query on MPD | H [auth A], I [auth A], J [auth A], P [auth B] | (4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N |  | ||
| PO4 Query on PO4 | G [auth A], O [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| CL Query on CL | E [auth A], M [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| OXY Query on OXY | F [auth A], N [auth B] | OXYGEN MOLECULE O2 MYMOFIZGZYHOMD-UHFFFAOYSA-N |  | ||
| NA Query on NA | D [auth A], L [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| TOX Query on TOX | A, B | L-PEPTIDE LINKING | C11 H12 N2 O4 |  | TRP |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.173 (Depositor), 0.180 (DCC)
- R-Value Work: 0.147 (Depositor), 0.160 (DCC)
- R-Value Observed: 0.148 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 100.896 | α = 90 |
| b = 113.257 | β = 90 |
| c = 174.598 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| MOLREP | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-02-21 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: 2018-02-21
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: 2023-11-15
Changes: Data collection
