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Yorodumi- PDB-5gzx: The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gzx | ||||||
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Title | The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA | ||||||
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-Chloropropionic acid / (R)-2-haloacid dehalogenase Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Wang, Y. / Xue, S. | ||||||
Citation | Journal: To Be Published Title: The complex structure of D-2-haloacid dehalogenase mutant with D-2-CPA 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 | 5gzx.cif.gz | 244.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gzx.ent.gz | 197.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gzx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gzx_validation.pdf.gz | 478.5 KB | Display | wwPDB validaton report |
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Full document | 5gzx_full_validation.pdf.gz | 496.5 KB | Display | |
Data in XML | 5gzx_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 5gzx_validation.cif.gz | 64.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/5gzx ftp://data.pdbj.org/pub/pdb/validation_reports/gz/5gzx | 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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1 |
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Unit cell |
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-Components
#1: Protein | ( Mass: 35084.996 Da / Num. of mol.: 4 / Mutation: D205N 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: Chemical | ChemComp-RCI / ( #3: 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: 2.55 Å3/Da / Density % sol: 51.77 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: PEG 20000, PEG 8000, MES, potassium sodium tartrate tetrahydrate, BaCl2 |
-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: 2.35→49.32 Å / Num. obs: 57707 / % possible obs: 98 % / Redundancy: 6.9 % / Net I/σ(I): 9.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3BJX Resolution: 2.35→49.32 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.38 / Phase error: 29.06
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→49.32 Å
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Refine LS restraints |
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LS refinement shell |
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