+Open data
-Basic information
Entry | Database: PDB / ID: 5syw | |||||||||
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Title | Crystal structure of Burkhoderia pseudomallei KatG variant Q233E | |||||||||
Components | Catalase-peroxidase | |||||||||
Keywords | OXIDOREDUCTASE / catalase-peroxidase / KatG / Q233E variant | |||||||||
Function / homology | Function and homology information catalase-peroxidase / catalase activity / hydrogen peroxide catabolic process / response to oxidative stress / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Burkholderia pseudomallei (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Loewen, P.C. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine. Authors: Machuqueiro, M. / Victor, B. / Switala, J. / Villanueva, J. / Rovira, C. / Fita, I. / Loewen, P.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5syw.cif.gz | 572.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5syw.ent.gz | 462.9 KB | Display | PDB format |
PDBx/mmJSON format | 5syw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/5syw ftp://data.pdbj.org/pub/pdb/validation_reports/sy/5syw | HTTPS FTP |
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-Related structure data
Related structure data | 5kq0C 5kq2C 5kq3C 5kq6C 5kqhC 5kqiC 5kqkC 5ksfC 5kskC 5syuC 5syvC 5txqC 5v4oC 5v53C 1mwv S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0
NCS ensembles :
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 79569.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain 1710b) (bacteria) Strain: 1710b / Gene: katG, BURPS1710b_3366 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JNW6, catalase-peroxidase |
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-Non-polymers , 7 types, 1473 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-MPD / ( #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16-20% PEG 4000, 20% MPD, 0.1 M sodium citrate pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→95.58 Å / Num. obs: 170117 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rsym value: 0.075 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 1.5 / Num. measured all: 91004 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1MWV 1mwv Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.759 / SU ML: 0.073 / SU R Cruickshank DPI: 0.0955 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.56 Å2 / Biso mean: 26.058 Å2 / Biso min: 14.18 Å2
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Refinement step | Cycle: final / Resolution: 1.85→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.85→1.898 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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