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Yorodumi- PDB-3wj8: Crystal Structure of DL-2-haloacid dehalogenase mutant with 2-bro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wj8 | ||||||
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Title | Crystal Structure of DL-2-haloacid dehalogenase mutant with 2-bromo-2-methylpropionate | ||||||
Components | DL-2-haloacid dehalogenase | ||||||
Keywords | HYDROLASE / dehalogenases | ||||||
Function / homology | 2-haloacid dehalogenase (configuration-inverting) / : / 2-bromo-2-methylpropanoic acid / DL-2-haloacid dehalogenase Function and homology information | ||||||
Biological species | Methylobacterium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Siwek, A. / Omi, R. / Hirotsu, K. / Jitsumori, K. / Esaki, N. / Kurihara, T. / Paneth, P. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2013 Title: Binding modes of DL-2-haloacid dehalogenase revealed by crystallography, modeling and isotope effects studies. Authors: Siwek, A. / Omi, R. / Hirotsu, K. / Jitsumori, K. / Esaki, N. / Kurihara, T. / Paneth, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wj8.cif.gz | 361.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wj8.ent.gz | 299.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wj8_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
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Full document | 3wj8_full_validation.pdf.gz | 510.6 KB | Display | |
Data in XML | 3wj8_validation.xml.gz | 71.7 KB | Display | |
Data in CIF | 3wj8_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/3wj8 ftp://data.pdbj.org/pub/pdb/validation_reports/wj/3wj8 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 34092.922 Da / Num. of mol.: 6 / Mutation: D54H, D194N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methylobacterium (bacteria) / Genus: dl-dex / Strain: CPA1 / Production host: Escherichia coli (E. coli) References: UniProt: A6BM74, 2-haloacid dehalogenase (configuration-inverting) #2: Chemical | ChemComp-B2P / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→161.35 Å / Num. obs: 61648 / % possible obs: 99.5 % |
-Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.86 / SU B: 13.519 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 16.812 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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