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Yorodumi- PDB-4cit: Crystal structure of the first bacterial vanadium dependant iodop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cit | ||||||
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Title | Crystal structure of the first bacterial vanadium dependant iodoperoxidase | ||||||
Components | VANADIUM-DEPENDENT HALOPEROXIDASE | ||||||
Keywords | TRANSFERASE / IODOPEROXIDASE / MARINE BACTERIUM | ||||||
Function / homology | Function and homology information Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity Similarity search - Function | ||||||
Biological species | ZOBELLIA GALACTANIVORANS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Rebuffet, E. / Delage, L. / Fournier, J.B. / Rzonca, J. / Potin, P. / Michel, G. / Czjzek, M. / Leblanc, C. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2014 Title: The Bacterial Vanadium Iodoperoxidase from the Marine Flavobacteriaceae Zobellia Galactanivorans Reveals Novel Molecular and Evolutionary Features of Halide Specificity in This Enzyme Family. Authors: Fournier, J.B. / Rebuffet, E. / Delage, L. / Grijol, R. / Meslet-Cladiere, L. / Rzonca, J. / Potin, P. / Michel, G. / Czjzek, M. / Leblanc, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cit.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cit.ent.gz | 79.6 KB | Display | PDB format |
PDBx/mmJSON format | 4cit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/4cit ftp://data.pdbj.org/pub/pdb/validation_reports/ci/4cit | 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
#1: Protein | Mass: 51543.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: VANADATE COFACTOR LINKED THROUGH HIS 416 / Source: (gene. exp.) ZOBELLIA GALACTANIVORANS (bacteria) Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) AND AVAILABLE AT STATION BIOLOGIQUE DE ROSCOFF, FRANCE Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: G0LAH5, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases, EC: 1.11.1.8 | ||||
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#2: Chemical | ChemComp-VO4 / #3: Chemical | ChemComp-NA / | #4: 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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: NONE |
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Crystal grow | pH: 4.2 Details: 1 MICROL OF ENZYME AND 0.5 MICROL OF RESERVOIR SOLUTION CONTAINING 23 % PEG 1150, 100 MM PHOSPHATE/CITRATE PH 4.2 AND 2 % GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2009 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 198448 / % possible obs: 99.2 % / Observed criterion σ(I): 0.1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.91 |
Reflection shell | Resolution: 1.8→1.85 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.74 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.8→20.01 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.789 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 16.797 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20.01 Å
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