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Yorodumi- PDB-7qyy: Vanadium-dependent bromoperoxidase from Corallina pilulifera in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qyy | ||||||
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Title | Vanadium-dependent bromoperoxidase from Corallina pilulifera in complex with chloride | ||||||
Components | Vanadium-dependent bromoperoxidase | ||||||
Keywords | OXIDOREDUCTASE / Vanadium protein / halogen binding / haloperoxidase. | ||||||
Function / homology | bromide peroxidase / bromide peroxidase activity / : / Bromoperoxidase/chloroperoxidase C-terminal / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily / metal ion binding / PHOSPHATE ION / Vanadium-dependent bromoperoxidase Function and homology information | ||||||
Biological species | Corallina pilulifera (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.999 Å | ||||||
Authors | Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: R396W mutant of the vanadium-dependent bromoperoxidase from Corallina pilulifera Authors: Isupov, M.N. / Mitchell, D. / Littelchild, J.A. / Garcia-Rodriguez, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qyy.cif.gz | 580.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qyy.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qy/7qyy ftp://data.pdbj.org/pub/pdb/validation_reports/qy/7qyy | HTTPS FTP |
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-Related structure data
Related structure data | 7qvwC 7qw3C 7qwiC 1up8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ILE / End label comp-ID: ILE / Auth seq-ID: 2 - 598 / Label seq-ID: 2 - 598
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 65343.949 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corallina pilulifera (eukaryote) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: O81959, bromide peroxidase |
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-Non-polymers , 6 types, 3313 molecules
#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 3.25 Å3/Da / Density % sol: 62.19 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-HBr, pH 7.4, 1.3M ammonium dihydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8482 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 15, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8482 Å / Relative weight: 1 |
Reflection | Resolution: 1.999→99 Å / Num. obs: 218890 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.999→2.07 Å / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 20725 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1up8 Resolution: 1.999→19.962 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.556 / SU ML: 0.093 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.134 / Details: Hydrogens have not been used
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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: BABINET MODEL PLUS MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.081 Å2
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Refinement step | Cycle: LAST / Resolution: 1.999→19.962 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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