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Yorodumi- PDB-4ixt: Structure of a 37-fold mutant of halohydrin dehalogenase (HheC) b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ixt | ||||||
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Title | Structure of a 37-fold mutant of halohydrin dehalogenase (HheC) bound to ethyl (R)-4-cyano-3-hydroxybutyrate | ||||||
Components | Halohydrin dehalogenase | ||||||
Keywords | LYASE / thermostability / synergistic mutations / coupled mutations / proline-induced / backbone changes / enantioselectivity changes / directed evolution / protein engineering / short-chain dehydrogenase/reductase enzyme superfamily / Cyanolysis / dehalogenase / Atorvastatin synthesis | ||||||
Function / homology | Function and homology information : / 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 / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Rhizobium radiobacter (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å | ||||||
Authors | Floor, R.J. / Schallmey, M. / Hauer, B. / Breuer, M. / Jekel, P.A. / Wijma, H.J. / Dijkstra, B.W. / Janssen, D.B. | ||||||
Citation | Journal: Chembiochem / Year: 2013 Title: Biocatalytic and structural properties of a highly engineered halohydrin dehalogenase. Authors: Schallmey, M. / Floor, R.J. / Hauer, B. / Breuer, M. / Jekel, P.A. / Wijma, H.J. / Dijkstra, B.W. / Janssen, D.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ixt.cif.gz | 107.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ixt.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ixt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ixt_validation.pdf.gz | 457.4 KB | Display | wwPDB validaton report |
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Full document | 4ixt_full_validation.pdf.gz | 461.3 KB | Display | |
Data in XML | 4ixt_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4ixt_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/4ixt ftp://data.pdbj.org/pub/pdb/validation_reports/ix/4ixt | HTTPS FTP |
-Related structure data
Related structure data | 4ixwC 4iy1C 1pwzS C: citing same article (ref.) 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: 27841.406 Da / Num. of mol.: 2 / Fragment: Halohydrin dehalogenase HheC Mutation: Q37H, K38Q, K52I, A60V, Y70L, Q72H, V75I, F82A, A83P, P84V, F86W, Q87R, G99D, A100M, R107K, V112A, K121R, T134A, P135S, T146A, C153S, T154A, Y166H, G174A, Y177G, L178V, H179D, E181G, F186Y, ...Mutation: Q37H, K38Q, K52I, A60V, Y70L, Q72H, V75I, F82A, A83P, P84V, F86W, Q87R, G99D, A100M, R107K, V112A, K121R, T134A, P135S, T146A, C153S, T154A, Y166H, G174A, Y177G, L178V, H179D, E181G, F186Y, T189S, N195S, V201W, K203R, V205Y, A222T, M245V, I246V Source method: isolated from a genetically manipulated source Details: This enzyme is a result of a directed evolution study. It contains 37 mutations, compared to its parent Source: (gene. exp.) Rhizobium radiobacter (bacteria) / Gene: hheC / Plasmid: pBAD-HheC-2360 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q93D82, Lyases; Carbon-halide lyases #2: Chemical | ChemComp-1H1 / | #3: Chemical | ChemComp-CL / | #4: 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: 2.98 Å3/Da / Density % sol: 58.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12.5% (w/v) PEG 8000,0.2 M Magnesium Chloride, 0.1 M Tris-Cl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 20, 2010 |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9395 Å / Relative weight: 1 |
Reflection | Resolution: 2.47→73.36 Å / Num. obs: 27496 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 7.3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PWZ Resolution: 2.49→52.34 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 7.415 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.364 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.067 Å2
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Refinement step | Cycle: LAST / Resolution: 2.49→52.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.49→2.553 Å / Total num. of bins used: 20
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