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Yorodumi- PDB-1nrw: The structure of a HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nrw | ||||||
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Title | The structure of a HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. SUBTILIS | ||||||
Components | hypothetical protein, haloacid dehalogenase-like hydrolaseHypothesis | ||||||
Keywords | HYDROLASE / structural genomics / Bacillus subtilis / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å | ||||||
Authors | Cuff, M.E. / Kim, Y. / Zhang, R. / Joachimiak, A. / Collart, F. / Quartey, P. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The structure of a HALOACID DEHALOGENASE-LIKE HYDROLASE FROM B. SUBTILIS Authors: Cuff, M.E. / Kim, Y. / Zhang, R. / Joachimiak, A. / Collart, F. / Quartey, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nrw.cif.gz | 79.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nrw.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 1nrw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/1nrw ftp://data.pdbj.org/pub/pdb/validation_reports/nr/1nrw | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32547.455 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: YWPJ / Production host: Escherichia coli (E. coli) / References: UniProt: P94592 | ||||
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#2: Chemical | #3: Chemical | ChemComp-CA / | #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: 2.2 Å3/Da / Density % sol: 43.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 400, sodium/potassium phosphate, sodium chloride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.K |
-Data collection
Diffraction | Mean temperature: 150 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948,0.97959,0.95372 | ||||||||||||
Detector | Type: SBC-2 / Detector: CCD / Date: Dec 19, 2002 | ||||||||||||
Radiation | Monochromator: sagitally focused Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.7→50 Å / Num. all: 38821 / Num. obs: 36714 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.1 Å2 / Limit h max: 31 / Limit h min: 0 / Limit k max: 40 / Limit k min: 0 / Limit l max: 54 / Limit l min: 0 / Observed criterion F max: 298130.29 / Observed criterion F min: 0.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.7→31.45 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.5 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: Bulk solvent / Bsol: 75.5048 Å2 / ksol: 0.369634 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.59 Å2 / Biso mean: 26.09 Å2 / Biso min: 9.36 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→31.45 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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Xplor file |
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