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Yorodumi- PDB-4ufp: Laboratory evolved variant R-C1B1D33 of potato epoxide hydrolase StEH1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ufp | ||||||
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Title | Laboratory evolved variant R-C1B1D33 of potato epoxide hydrolase StEH1 | ||||||
Components | EPOXIDE HYDROLASE | ||||||
Keywords | HYDROLASE / EPOXIDE HYDROLYSIS / ALPHA/BETA-HYDROLASE / DIRECTED EVOLUTION / ASYMMETRIC SYNTHESES | ||||||
Function / homology | Function and homology information | ||||||
Biological species | SOLANUM TUBEROSUM (potato) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Carlsson, A.J. / Bauer, P. / Nilsson, M. / Dobritzsch, D. / Kamerlin, S.C.L. / Widersten, M. | ||||||
Citation | Journal: Chembiochem / Year: 2016 Title: Laboratory Evolved Enzymes Provide Snapshots of the Development of Enantioconvergence in Enzyme-Catalyzed Epoxide Hydrolysis. Authors: Janfalk Carlsson, A. / Bauer, P. / Dobritzsch, D. / Nilsson, M. / Kamerlin, S.C. / Widersten, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ufp.cif.gz | 135.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ufp.ent.gz | 107.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ufp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uf/4ufp ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4ufp | HTTPS FTP |
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-Related structure data
Related structure data | 4ufoC 4uhbC 2cjpS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 3 - 321 / Label seq-ID: 3 - 321
NCS oper: (Code: given Matrix: (0.6997, 0.6946, 0.1673), Vector: |
-Components
#1: Protein | Mass: 37130.555 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Strain: LEMHI RUSSET / Plasmid: PGTACSTEH1-5H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: Q41415, epoxide hydrolase #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS C-TERMINALLY HIS-TAGGED AND IS MUTATED AT 6 POSITIONS (P84L, W106L, L109Y, V141K, ...THE SEQUENCE IS C-TERMINALLY | |
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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: 2.3 Å3/Da / Density % sol: 46.2 % / Description: NONE |
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Crystal grow | pH: 9 / Details: 10% (W/V) PEG10K, 0.1 M BICINE PH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→75.9 Å / Num. obs: 13146 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.95→3.13 Å / Redundancy: 6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 0.4 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CJP Resolution: 2.95→75.9 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.534 / SU ML: 0.334 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 51.566 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→75.9 Å
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Refine LS restraints |
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