+Open data
-Basic information
Entry | Database: PDB / ID: 5y5d | ||||||
---|---|---|---|---|---|---|---|
Title | The crystal structure of VrEH2 mutant M263W | ||||||
Components | Epoxide hydrolase | ||||||
Keywords | HYDROLASE / Epoxide hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vigna radiata (mung bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Xu, J.H. / Yu, H.L. / Zhou, J.H. / Kong, X.D. / Li, F.L. | ||||||
Citation | Journal: To Be Published Title: The crystal structure of VrEH2 mutant M263W Authors: Xu, J.H. / Yu, H.L. / Zhou, J.H. / Kong, X.D. / Li, F.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5y5d.cif.gz | 85.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5y5d.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 5y5d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/5y5d ftp://data.pdbj.org/pub/pdb/validation_reports/y5/5y5d | HTTPS FTP |
---|
-Related structure data
Related structure data | 5xm6S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 37388.359 Da / Num. of mol.: 1 / Mutation: G3F, V4I, M263W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vigna radiata (mung bean) / Gene: EH2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0R5NGA4 |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % / Description: rhombus |
---|---|
Crystal grow | Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG3350, Tris-HCL, Ethylene glycol. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 28594 / % possible obs: 99.7 % / Observed criterion σ(I): 0.9 / Redundancy: 24.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 38.444 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.866 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 28594 / Rsym value: 0.866 / % possible all: 96 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XM6 Resolution: 1.85→25.422 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.29
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→25.422 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|