+Open data
-Basic information
Entry | Database: PDB / ID: 5gkw | ||||||
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Title | crystal structure of SZ529 complex with (R,R)-cyclopentanediol | ||||||
Components | Limonene-1,2-epoxide hydrolase | ||||||
Keywords | HYDROLASE / mutant R / R-selectivity | ||||||
Function / homology | Function and homology information limonene-1,2-epoxide hydrolase / limonene-1,2-epoxide hydrolase activity Similarity search - Function | ||||||
Biological species | Rhodococcus erythropolis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å | ||||||
Authors | Wu, L. / Sun, Z.T. / Reetz, M.T. / Zhou, J.H. | ||||||
Citation | Journal: To Be Published Title: crystal structure of SZ529 complex with (R,R)-cyclopentanediol Authors: Wu, L. / Sun, Z.T. / Reetz, M.T. / Zhou, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gkw.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gkw.ent.gz | 96.8 KB | Display | PDB format |
PDBx/mmJSON format | 5gkw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gkw_validation.pdf.gz | 458.6 KB | Display | wwPDB validaton report |
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Full document | 5gkw_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 5gkw_validation.xml.gz | 14 KB | Display | |
Data in CIF | 5gkw_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/5gkw ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gkw | HTTPS FTP |
-Related structure data
Related structure data | 5cf1S 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17319.320 Da / Num. of mol.: 2 / Fragment: UNP residues 2-149 / Mutation: M32V/M78V/I80V/L114F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Gene: limA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9ZAG3, limonene-1,2-epoxide hydrolase #2: Chemical | ChemComp-6VV / ( | #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: 2.84 Å3/Da / Density % sol: 54.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.4M sodium citrate, 0.1M Hepes pH 7.0 / PH range: 6.5-7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.93911 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 17, 2015 |
Radiation | Monochromator: si III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93911 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 26234 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/av σ(I): 1.4 / Net I/σ(I): 12.365 |
Reflection shell | Resolution: 2.01→2.08 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.772 / Mean I/σ(I) obs: 2.5 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5CF1 Resolution: 2.01→47.556 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.47 / 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: 2.01→47.556 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.6343 Å / Origin y: 81.2832 Å / Origin z: 145.6554 Å
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Refinement TLS group | Selection details: all |