+Open data
-Basic information
Entry | Database: PDB / ID: 2zpb | ||||||
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Title | nitrosylated Fe-type nitrile hydratase | ||||||
Components | (Nitrile hydratase subunit ...) x 2 | ||||||
Keywords | LYASE / Iron / Metal-binding / Oxidation | ||||||
Function / homology | Function and homology information nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hashimoto, K. / Suzuki, H. / Taniguchi, K. / Noguchi, T. / Yohda, M. / Odaka, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile Authors: Hashimoto, K. / Suzuki, H. / Taniguchi, K. / Noguchi, T. / Yohda, M. / Odaka, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zpb.cif.gz | 115.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zpb.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 2zpb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zpb ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zpb | HTTPS FTP |
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-Related structure data
Related structure data | 2zpeC 2zpfC 2zpgC 2zphC 2zpiC 2ahjS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Nitrile hydratase subunit ... , 2 types, 2 molecules AB
#1: Protein | Mass: 22933.873 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: N771 / References: UniProt: P13448, nitrile hydratase |
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#2: Protein | Mass: 23514.303 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodococcus erythropolis (bacteria) / Strain: N771 / References: UniProt: P13449, nitrile hydratase |
-Non-polymers , 4 types, 783 molecules
#3: Chemical | ChemComp-FE / | ||
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#4: Chemical | ChemComp-NO / | ||
#5: Chemical | #6: 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: 2.51 Å3/Da / Density % sol: 50.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% PEG 8000, 0.1M Tris-HCl PH7.5, 300mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 21, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→67.116 Å / Num. obs: 113080 / % possible obs: 98.8 % / Biso Wilson estimate: 10.7 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AHJ Resolution: 1.3→7.96 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.695 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.122 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→7.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.299→1.332 Å / Total num. of bins used: 20
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