+Open data
-Basic information
Entry | Database: PDB / ID: 5h01 | ||||||
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Title | The crystal structure of D-2-halacid dehalogenase mutant | ||||||
Components | (R)-2-haloacid dehalogenase | ||||||
Keywords | HYDROLASE / dehalogenation / D-2-haloacid dehalogenase | ||||||
Function / homology | (R)-2-haloacid dehalogenase / (R)-2-haloacid dehalogenase activity / 2-haloacid dehalogenase, DehI / Halocarboxylic acid dehydrogenase DehI / AhpD-like / (R)-2-haloacid dehalogenase Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.194 Å | ||||||
Authors | Xue, S. / Wang, Y. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of D-2-halacid dehalogenase mutant Authors: Xue, S. / Wang, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h01.cif.gz | 243.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h01.ent.gz | 198 KB | Display | PDB format |
PDBx/mmJSON format | 5h01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h01 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h01 | HTTPS FTP |
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-Related structure data
Related structure data | 3bjxS 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: 35085.980 Da / Num. of mol.: 4 / Mutation: L288I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: hadD / Production host: Escherichia coli (E. coli) / References: UniProt: Q52086, (R)-2-haloacid dehalogenase #2: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.34 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: MES, PEG 20000, PEG 8000, potassium sodium tartrate tetrahydrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→48.591 Å / Num. obs: 75088 / % possible obs: 95.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.178 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.19→2.23 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BJX Resolution: 2.194→48.591 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.194→48.591 Å
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Refine LS restraints |
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LS refinement shell |
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