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Yorodumi- PDB-4izs: The C145A mutant of the amidase from Nesterenkonia sp. AN1 in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4izs | ||||||
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Title | The C145A mutant of the amidase from Nesterenkonia sp. AN1 in complex with butyramide | ||||||
Components | Amidase | ||||||
Keywords | HYDROLASE / butyramide | ||||||
Function / homology | Function and homology information amidase / indoleacetamide hydrolase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / amidase activity Similarity search - Function | ||||||
Biological species | Nesterenkonia sp. 10004 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å | ||||||
Authors | Kimani, S.W. / Sewell, B.T. | ||||||
Citation | Journal: To be Published Title: Covalent modifications of the active site cysteine occur as a result of mutating the glutamate of the catalytic triad in the amidase from Nesterenkonia sp. Authors: Kimani, S.W. / Hunter, R. / Vlok, M. / Watermeyer, J. / Sewell, B.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4izs.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4izs.ent.gz | 51.6 KB | Display | PDB format |
PDBx/mmJSON format | 4izs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4izs_validation.pdf.gz | 452.8 KB | Display | wwPDB validaton report |
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Full document | 4izs_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 4izs_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 4izs_validation.cif.gz | 22.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/4izs ftp://data.pdbj.org/pub/pdb/validation_reports/iz/4izs | HTTPS FTP |
-Related structure data
Related structure data | 4iztC 4izuC 4izvC 4izwC 3hkxS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 30068.686 Da / Num. of mol.: 1 / Mutation: C145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VWZ1, amidase | ||||
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#2: Chemical | #3: Chemical | ChemComp-BMD / | #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: 2.34 Å3/Da / Density % sol: 47.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium, 2% PEG 400, 2.0 M ammonium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.44→22.951 Å / Num. all: 51279 / Num. obs: 51279 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rsym value: 0.069 / Net I/σ(I): 15.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 26.24 / Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HKX Resolution: 1.44→22.95 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.1793 / WRfactor Rwork: 0.1601 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9061 / SU B: 0.852 / SU ML: 0.033 / SU R Cruickshank DPI: 0.0563 / SU Rfree: 0.0568 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.057 / 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: 57.22 Å2 / Biso mean: 15.7782 Å2 / Biso min: 5.65 Å2
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Refinement step | Cycle: LAST / Resolution: 1.44→22.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.44→1.477 Å / Total num. of bins used: 20
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