+Open data
-Basic information
Entry | Database: PDB / ID: 5h00 | ||||||
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Title | The crystal structure of D-2-haloacid dehalogenase | ||||||
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: 2.64 Å | ||||||
Authors | Wang, Y. / Xue, S. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of D-2-haloacid dehalogenase Authors: Wang, Y. / Xue, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h00.cif.gz | 236.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h00.ent.gz | 191.9 KB | Display | PDB format |
PDBx/mmJSON format | 5h00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h00_validation.pdf.gz | 453.2 KB | Display | wwPDB validaton report |
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Full document | 5h00_full_validation.pdf.gz | 463.5 KB | Display | |
Data in XML | 5h00_validation.xml.gz | 43.6 KB | Display | |
Data in CIF | 5h00_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/5h00 ftp://data.pdbj.org/pub/pdb/validation_reports/h0/5h00 | HTTPS FTP |
-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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Unit cell |
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-Components
#1: Protein | ( Mass: 34014.840 Da / Num. of mol.: 4 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: 2.78 Å3/Da / Density % sol: 55.7 % |
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Crystal grow | Temperature: 277 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: BL18U1 / Wavelength: 0.97776 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 2.64→45.24 Å / Num. obs: 42453 / % possible obs: 97.8 % / Redundancy: 8.4 % / Net I/σ(I): 9.73 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BJX Resolution: 2.64→45.24 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.64→45.24 Å
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Refine LS restraints |
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LS refinement shell |
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