+Open data
-Basic information
Entry | Database: PDB / ID: 3hkx | ||||||
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Title | Crystal structure analysis of an amidase from Nesterenkonia sp. | ||||||
Components | Amidase | ||||||
Keywords | HYDROLASE / ALPHA-BETA-BETA-ALPHA:ALPHA-BETA-BETA-ALPHA DIMERIC SANDWICH | ||||||
Function / homology | Function and homology information amidase / indoleacetamide hydrolase activity / organonitrogen compound metabolic process / amidase activity Similarity search - Function | ||||||
Biological species | Nesterenkonia sp. 10004 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.66 Å | ||||||
Authors | Sewell, B.T. / Nel, A.J.M. / Cowan, D.A. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2011 Title: Unique aliphatic amidase from a psychrotrophic and haloalkaliphilic nesterenkonia isolate. Authors: Nel, A.J. / Tuffin, I.M. / Sewell, B.T. / Cowan, D.A. #1: Journal: Thesis / Year: 2009 Title: Isolation of a novel cold-adapted nitrile hydrolysing micro-organism Authors: Nel, A.J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hkx.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hkx.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hkx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hk/3hkx ftp://data.pdbj.org/pub/pdb/validation_reports/hk/3hkx | HTTPS FTP |
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-Related structure data
Related structure data | 1f89S 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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-Components
#1: Protein | Mass: 30116.795 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nesterenkonia sp. 10004 (bacteria) / Strain: AN1 / Gene: Nit2 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: D0VWZ1, amidase |
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#2: 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: 2.39 Å3/Da / Density % sol: 48.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1M Sodium acetate trihydrate and 2M ammonium sulphate, pH 4.6, vapor diffusion, hanging drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 123 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9778 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 25, 2009 Details: J. Synchrotron Rad. (1999). 6, 822-833 Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities A. Cassetta, A. M. Deacon, S. ...Details: J. Synchrotron Rad. (1999). 6, 822-833 Development of instrumentation and methods for MAD and structural genomics at the SRS, ESRF, CHESS and Elettra facilities A. Cassetta, A. M. Deacon, S. E. Ealick, J. R. Helliwell and A. W. Thompson | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 7.03 % / Number: 242641 / Rmerge(I) obs: 0.046 / Χ2: 0.94 / D res high: 1.66 Å / D res low: 38 Å / Num. obs: 34232 / % possible obs: 99.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | ID: 1
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Reflection | Resolution: 1.66→63.511 Å / Num. all: 34246 / Num. obs: 34232 / % possible obs: 99.9 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.03 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 1.66→1.72 Å / Redundancy: 6.92 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 26.9 / 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: PDB entry 1F89 Resolution: 1.66→63.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0 / SU B: 1.835 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.094 / 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: 25.576 Å2
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Refinement step | Cycle: LAST / Resolution: 1.66→63.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.66→1.703 Å / Total num. of bins used: 20
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