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Yorodumi- PDB-1vnh: CHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS: MUTANT H496A -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vnh | ||||||
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Title | CHLOROPEROXIDASE FROM THE FUNGUS CURVULARIA INAEQUALIS: MUTANT H496A | ||||||
Components | VANADIUM CHLOROPEROXIDASE | ||||||
Keywords | HALOPEROXIDASE / VANADIUM-CONTAINING HALOPEROXIDASE / OXIDOREDUCTASE / MUTANT H496A | ||||||
Function / homology | Function and homology information chloride peroxidase / chloride peroxidase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Curvularia inaequalis (fungus) | ||||||
Method | X-RAY DIFFRACTION / OTHER / Resolution: 2.11 Å | ||||||
Authors | Macedo-Ribeiro, S. / Messerschmidt, A. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 1999 Title: X-ray crystal structures of active site mutants of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis. Authors: Macedo-Ribeiro, S. / Hemrika, W. / Renirie, R. / Wever, R. / Messerschmidt, A. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996 Title: X-Ray Structure of a Vanadium-Containing Enzyme: Chloroperoxidase from the Fungus Curvularia Inaequalis Authors: Messerschmidt, A. / Wever, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vnh.cif.gz | 127.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vnh.ent.gz | 98.8 KB | Display | PDB format |
PDBx/mmJSON format | 1vnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/1vnh ftp://data.pdbj.org/pub/pdb/validation_reports/vn/1vnh | HTTPS FTP |
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-Related 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: 67560.375 Da / Num. of mol.: 1 / Mutation: H496A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Curvularia inaequalis (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P49053, chloride peroxidase |
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#2: Chemical | ChemComp-VO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Date: Jun 1, 1998 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→15 Å / Num. obs: 40714 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.11→2.16 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 0.6 / % possible all: 75.6 |
Reflection | *PLUS Num. measured all: 112709 / Rmerge(I) obs: 0.087 |
Reflection shell | *PLUS % possible obs: 75.6 % / Rmerge(I) obs: 0.447 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.11→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE VANADATE ION WAS REFINED WITH A TETRAHEDRAL CONFORMATION
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Displacement parameters | Biso mean: 29.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.11→8 Å
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Refine LS restraints |
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Refinement | *PLUS Rfactor obs: 0.188 / Rfactor Rfree: 0.219 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 2.11 Å / Lowest resolution: 2.16 Å / Rfactor Rfree: 0.372 / Rfactor obs: 0.325 |