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Yorodumi- PDB-2vcn: Structure of isoniazid (INH) bound to cytosolic soybean ascorbate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vcn | ||||||
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Title | Structure of isoniazid (INH) bound to cytosolic soybean ascorbate peroxidase mutant W41A | ||||||
Components | ASCORBATE PEROXIDASE | ||||||
Keywords | OXIDOREDUCTASE / ASCORBATE PEROXIDASE / INH / APX / ISONIAZID / PEROXIDASE | ||||||
Function / homology | Function and homology information L-ascorbate peroxidase / L-ascorbate peroxidase activity / chloroplast / response to reactive oxygen species / hydrogen peroxide catabolic process / cellular response to oxidative stress / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | GLYCINE MAX (soybean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Metcalfe, C.L. / Macdonald, I.K. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: The Tuberculosis Prodrug Isoniazid Bound to Activating Peroxidases. Authors: Metcalfe, C.L. / Macdonald, I.K. / Murphy, E.J. / Brown, K.A. / Raven, E.L. / Moody, P.C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vcn.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vcn.ent.gz | 91.4 KB | Display | PDB format |
PDBx/mmJSON format | 2vcn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vcn_validation.pdf.gz | 833.3 KB | Display | wwPDB validaton report |
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Full document | 2vcn_full_validation.pdf.gz | 836.9 KB | Display | |
Data in XML | 2vcn_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 2vcn_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/2vcn ftp://data.pdbj.org/pub/pdb/validation_reports/vc/2vcn | HTTPS FTP |
-Related structure data
Related structure data | 2v23C 2v2eC 2vcfC 2vcsC 1oafS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28246.775 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-250 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) GLYCINE MAX (soybean) / Plasmid: SAPX4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SG13009 / References: UniProt: Q43758, L-ascorbate peroxidase | ||||||
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#2: Chemical | ChemComp-HEM / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 38.98 % / Description: NONE |
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Crystal grow | pH: 8.3 / Details: pH 8.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→37.58 Å / Num. obs: 78730 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 1.2→1.26 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.5 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OAF Resolution: 1.2→36.74 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.802 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.053 / ESU R Free: 0.049 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.66 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→36.74 Å
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Refine LS restraints |
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