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Yorodumi- PDB-7qou: A mutant of the nitrile hydratase from Geobacillus pallidus havin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qou | ||||||
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Title | A mutant of the nitrile hydratase from Geobacillus pallidus having enhanced thermostability | ||||||
Components |
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Keywords | LYASE / heterotetramer | ||||||
Function / homology | Function and homology information nitrile hydratase / indole-3-acetonitrile nitrile hydratase activity / transition metal ion binding Similarity search - Function | ||||||
Biological species | Aeribacillus pallidus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Van Wyk, J.C. / Cowan, D.A. / Danson, M.J. / Tsekoa, T.L. / Sayed, M.F. / Sewell, B.T. | ||||||
Funding support | South Africa, 1items
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Citation | Journal: Curr Res Struct Biol / Year: 2022 Title: Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase. Authors: Van Wyk, J.C. / Sewell, B.T. / Danson, M.J. / Tsekoa, T.L. / 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 | 7qou.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qou.ent.gz | 160 KB | Display | PDB format |
PDBx/mmJSON format | 7qou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qou_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7qou_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7qou_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7qou_validation.cif.gz | 32.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/7qou ftp://data.pdbj.org/pub/pdb/validation_reports/qo/7qou | HTTPS FTP |
-Related structure data
Related structure data | 7qopC 7qovC 7z0vC 2dppS 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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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 24700.178 Da / Num. of mol.: 1 / Fragment: chain A / Mutation: M188V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeribacillus pallidus (bacteria) / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84FS5, nitrile hydratase |
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#2: Protein | Mass: 26562.209 Da / Num. of mol.: 1 / Fragment: chain B / Mutation: D96E, D167V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeribacillus pallidus (bacteria) / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84FS6, nitrile hydratase |
-Non-polymers , 4 types, 395 molecules
#3: Chemical | ChemComp-CO / | ||||
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#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-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: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 30% PEG400, 100mM magnesium chloride, 100mM MES (2[N-Morpholino]ethanesulfonic acid), 10-40mg/ml protein, pH 6.5, vapor diffusion, hanging drop, temperature 295K |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2007 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→74.95 Å / Num. obs: 294741 / % possible obs: 98.5 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.046 / Χ2: 0.96 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 3.33 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3 / Num. unique obs: 86186 / Χ2: 1.42 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2dpp Resolution: 1.3→74.95 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.556 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.047 / ESU R Free: 0.046 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||
Displacement parameters | Biso max: 53.99 Å2 / Biso mean: 12.672 Å2 / Biso min: 7.65 Å2
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Refinement step | Cycle: final / Resolution: 1.3→74.95 Å
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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