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Yorodumi- PDB-4c50: Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c50 | ||||||
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Title | Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant from Mycobacterium Tuberculosis | ||||||
Components | CATALASE-PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / cell wall / catalase activity / NADPH binding / positive regulation of DNA repair / peroxidase activity / peptidoglycan-based cell wall ...oxidoreductase activity, acting on a heme group of donors, nitrogenous group as acceptor / Tolerance of reactive oxygen produced by macrophages / catalase-peroxidase / NADH binding / cell wall / catalase activity / NADPH binding / positive regulation of DNA repair / peroxidase activity / peptidoglycan-based cell wall / hydrogen peroxide catabolic process / cellular response to hydrogen peroxide / response to oxidative stress / response to antibiotic / heme binding / extracellular region / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hersleth, H.-P. / Zhao, X. / Magliozzo, R.S. / Andersson, K.K. | ||||||
Citation | Journal: Chem.Commun.(Camb.) / Year: 2013 Title: Access Channel Residues Ser315 and Asp137 in Mycobacterium Tuberculosis Catalase-Peroxidase (Katg) Control Peroxidatic Activation of the Pro-Drug Isoniazid. Authors: Zhao, X. / Hersleth, H.P. / Zhu, J. / Andersson, K.K. / Magliozzo, R.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c50.cif.gz | 283.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c50.ent.gz | 228.6 KB | Display | PDB format |
PDBx/mmJSON format | 4c50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c5/4c50 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/4c50 | HTTPS FTP |
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-Related structure data
Related structure data | 4c51C 2ccaS C: citing same article (ref.) S: Starting model for refinement |
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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: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 1 / Auth seq-ID: 25 - 740 / Label seq-ID: 25 - 740
NCS oper:
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-Components
#1: Protein | Mass: 80659.602 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MYW-ADDUCT BETWEEN M255 Y229 W107 / Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q08129, UniProt: P9WIE5*PLUS, catalase-peroxidase #2: Sugar | ChemComp-GLC / | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: 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: 2.83 Å3/Da / Density % sol: 56.3 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 100 MM SODIUM ACETATE, PH 4.6, 6% PEG 4000, AND 0.17 MM N-DODECYL-BETA-D-MALTOSIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→75.3 Å / Num. obs: 62942 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 6.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CCA Resolution: 2.5→75.41 Å / Cor.coef. Fo:Fc: 0.876 / Cor.coef. Fo:Fc free: 0.824 / SU B: 15.465 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R: 0.587 / ESU R Free: 0.344 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.25 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→75.41 Å
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