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Yorodumi- PDB-3bb0: Crystal Structure of a Trapped Phosphate-Intermediate in Vanadium... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bb0 | ||||||
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Title | Crystal Structure of a Trapped Phosphate-Intermediate in Vanadium Apochloroperoxidase Catalyzing a Dephosphorylation Reaction | ||||||
Components | Vanadium chloroperoxidase | ||||||
Keywords | OXIDOREDUCTASE / Protein phosphate-intermediate complex / phospatase activity / Chloride / Metal-binding / Peroxidase / Secreted / Vanadium | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Messerschmidt, A. / Macedo-Ribeiro, S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Crystal structure of a trapped phosphate intermediate in vanadium apochloroperoxidase catalyzing a dephosphorylation reaction Authors: Macedo-Ribeiro, S. / 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. #2: 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bb0.cif.gz | 145.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bb0.ent.gz | 111.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bb/3bb0 ftp://data.pdbj.org/pub/pdb/validation_reports/bb/3bb0 | HTTPS FTP |
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-Related structure data
Related structure data | 1vnsS 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: 67671.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Curvularia inaequalis (fungus) / Gene: CPO / Plasmid: pTNT14 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): BJ1991 / References: UniProt: P49053, chloride peroxidase | ||||
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#2: Chemical | ChemComp-PO3 / | ||||
#3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THIS CONFLICT MAY BE A SEQUENCING ERROR (THE CODON FOR ARG VARIES BY ONE NUCLEOTIDE CHANGE WITH PRO ...THIS CONFLICT MAY BE A SEQUENCING | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 3 micro-l of protein solution (5mg/ml in 5mM MOPS, pH 7.5), 3 micro-l precipitating buffer (1.7M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, 0.3 micro-l 10mM cysteine-HCl) , VAPOR DIFFUSION, ...Details: 3 micro-l of protein solution (5mg/ml in 5mM MOPS, pH 7.5), 3 micro-l precipitating buffer (1.7M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, 0.3 micro-l 10mM cysteine-HCl) , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 14, 1998 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 101188 / Num. obs: 100278 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.062 / Rsym value: 0.062 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5046 / Rsym value: 0.317 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VNS Resolution: 1.5→14.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.066 / SU ML: 0.041 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.071 / ESU R Free: 0.07 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.863 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→14.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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