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Yorodumi- PDB-5b12: Crystal structure of the B-type halohydrin hydrogen-halide-lyase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b12 | ||||||
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Title | Crystal structure of the B-type halohydrin hydrogen-halide-lyase mutant F71W/Q125T/D199H from Corynebacterium sp. N-1074 | ||||||
Components | Halohydrin epoxidase B | ||||||
Keywords | LYASE / Enantioselectivity / Halohydrin | ||||||
Function / homology | Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / metal ion binding / Alpha Beta / Halohydrin epoxidase B Function and homology information | ||||||
Biological species | Corynebacterium sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.721 Å | ||||||
Authors | Watanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Yohda, M. | ||||||
Citation | Journal: J.Biosci.Bioeng. / Year: 2016 Title: Improvement of enantioselectivity of the B-type halohydrin hydrogen-halide-lyase from Corynebacterium sp. N-1074 Authors: Watanabe, F. / Yu, F. / Ohtaki, A. / Yamanaka, Y. / Noguchi, K. / Odaka, M. / Yohda, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b12.cif.gz | 302.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b12.ent.gz | 244.2 KB | Display | PDB format |
PDBx/mmJSON format | 5b12.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5b12_validation.pdf.gz | 452.4 KB | Display | wwPDB validaton report |
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Full document | 5b12_full_validation.pdf.gz | 456.9 KB | Display | |
Data in XML | 5b12_validation.xml.gz | 62 KB | Display | |
Data in CIF | 5b12_validation.cif.gz | 93.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/5b12 ftp://data.pdbj.org/pub/pdb/validation_reports/b1/5b12 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25358.500 Da / Num. of mol.: 6 / Fragment: UNP residues 11-235 / Mutation: F71W, Q125T, D199H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium sp. (bacteria) / Gene: hheB / Plasmid: pSTT206 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q46347 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.08 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG400, ammonium sulfate, 2-propanol, PEPES |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 17, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. obs: 143723 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rsym value: 0.09 / Net I/σ(I): 37.4 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 11.6 / % possible all: 100 |
-Processing
Software |
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Refinement | Resolution: 1.721→35.13 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.49 / 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: 1.721→35.13 Å
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Refine LS restraints |
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LS refinement shell |
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