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Yorodumi- PDB-2dpp: Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratase -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dpp | ||||||
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Title | Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratase | ||||||
Components |
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Keywords | LYASE / nitrile hydratase / cobalt / oxidised cys | ||||||
Function / homology | Function and homology information nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus sp. RAPc8 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Tsekoa, T.L. / Tastan-Bishop, A.O. / Cameron, R.A. / Sewell, B.T. / Sayed, M.F. / Cowan, D.A. | ||||||
Citation | Journal: To be Published Title: Crystal structure of thermostable Bacillus sp. RAPc8 nitrile hydratse Authors: Tsekoa, T.L. / Tastan-Bishop, A.O. / Cameron, R.A. / Sewell, B.T. / Sayed, M.F. / Cowan, D.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2dpp.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dpp.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 2dpp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/2dpp ftp://data.pdbj.org/pub/pdb/validation_reports/dp/2dpp | HTTPS FTP |
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-Related structure data
Related structure data | 1ireS 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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Details | The biological assembly is a tetramer generated from the dimer in the assymetric unit. The dimers interact along a two-fold crystallographic axis. |
-Components
#1: Protein | Mass: 24716.244 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase, alpha chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. RAPc8 (bacteria) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q84FS5, nitrile hydratase |
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#2: Protein | Mass: 26564.139 Da / Num. of mol.: 1 / Fragment: Nitrile hydratase, beta chain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus sp. RAPc8 (bacteria) / Plasmid: pET21a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q84FS6, nitrile hydratase |
#3: Chemical | ChemComp-CO / |
#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: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG 400, 0.1M MES, 0.1M magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2004 / Details: AXCO PX50 glass capillary optic with a 0.1mm focus |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→20 Å / Num. obs: 16152 / Rmerge(I) obs: 0.091 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IRE Resolution: 2.52→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.879 / SU B: 9.561 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.938 / ESU R Free: 0.346 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2.52→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.584 Å / Total num. of bins used: 20
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