[English] 日本語
Yorodumi- PDB-4wy5: Structural analysis of two fungal esterases from Rhizomucor miehe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4wy5 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural analysis of two fungal esterases from Rhizomucor miehei explaining their substrate specificity | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / Rhizomucor miehei / Esterase / Substrate specificity | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rhizomucor miehei (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Qin, Z. / Yang, S. / Duan, X. / Yan, Q. / Jiang, Z. | ||||||
Citation | Journal: J.Lipid Res. / Year: 2015 Title: Structural insights into the substrate specificity of two esterases from the thermophilic Rhizomucor miehei Authors: Yang, S. / Qin, Z. / Duan, X. / Yan, Q. / Jiang, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4wy5.cif.gz | 137 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4wy5.ent.gz | 107.6 KB | Display | PDB format |
PDBx/mmJSON format | 4wy5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4wy5_validation.pdf.gz | 449.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4wy5_full_validation.pdf.gz | 455.9 KB | Display | |
Data in XML | 4wy5_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 4wy5_validation.cif.gz | 37.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wy/4wy5 ftp://data.pdbj.org/pub/pdb/validation_reports/wy/4wy5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36104.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhizomucor miehei (fungus) / Plasmid: PET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: V5J5W4, carboxylesterase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.74 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 25% (w/v)PEG3350; 0.2M (NH4)2SO4; 0.1M MES buffer pH6.0 |
-Data collection
Diffraction | Mean temperature: 90 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9791 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 15, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→31.8 Å / Num. obs: 26738 / % possible obs: 94.01 % / Redundancy: 2 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.92 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→31.8 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 24.56 / Stereochemistry target values: ML Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→31.8 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|