[English] 日本語
Yorodumi- PDB-4lye: Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lye | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the S105A mutant of a C-C hydrolase, DxnB2 from Sphingomonas wittichii RW1, in complex with substrate HOPDA | ||||||
Components | MCP Hydrolase | ||||||
Keywords | HYDROLASE / meta-cleavage product hydrolase / C-C bond hydrolase / alpha-beta hydrolase / dibenzo-p-dioxin degradation / dibenzofuran degradation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Sphingomonas wittichii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.33 Å | ||||||
Authors | Ghosh, S. / Bolin, J.T. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: A substrate-assisted mechanism of nucleophile activation in a ser-his-asp containing C-C bond hydrolase. Authors: Ruzzini, A.C. / Bhowmik, S. / Ghosh, S. / Yam, K.C. / Bolin, J.T. / Eltis, L.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4lye.cif.gz | 66.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4lye.ent.gz | 49.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lye.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4lye ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4lye | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30208.531 Da / Num. of mol.: 1 / Mutation: S105A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sphingomonas wittichii (bacteria) / Strain: RW1 / Gene: dxnB2, Swit_3055 / Plasmid: pEMDXN1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a References: UniProt: A5VAT9, 2,6-dioxo-6-phenylhexa-3-enoate hydrolase |
---|---|
#2: Chemical | ChemComp-HPK / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.5 Å3/Da / Density % sol: 64.86 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: 1.8 M sodium malonate, pH 6.8, vapor diffusion, sitting drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→50 Å / Num. obs: 19800 / % possible obs: 99.5 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.09 / Χ2: 1.187 / Net I/σ(I): 11.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Rfactor: 44.21 / Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.33→21.14 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.2383 / WRfactor Rwork: 0.1889 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8241 / SU B: 6.332 / SU ML: 0.143 / SU R Cruickshank DPI: 0.2068 / SU Rfree: 0.1904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.207 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 112.24 Å2 / Biso mean: 48.3882 Å2 / Biso min: 17.21 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.33→21.14 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.33→2.39 Å / Total num. of bins used: 20
|