+Open data
-Basic information
Entry | Database: PDB / ID: 3wl7 | ||||||
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Title | The complex structure of pOPH S172C with ligand, ACA | ||||||
Components | Oxidized polyvinyl alcohol hydrolase | ||||||
Keywords | HYDROLASE / alpha/beta-hydrolase / oxi-polyvinyl alcohol hydrolase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Yang, Y. / Ko, T.P. / Li, J.H. / Liu, L. / Huang, C.H. / Chan, H.C. / Ren, F.F. / Jia, D.X. / Wang, A.H.-J. / Guo, R.T. ...Yang, Y. / Ko, T.P. / Li, J.H. / Liu, L. / Huang, C.H. / Chan, H.C. / Ren, F.F. / Jia, D.X. / Wang, A.H.-J. / Guo, R.T. / Chen, J. / Du, G.C. | ||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Structural insights into enzymatic degradation of oxidized polyvinyl alcohol Authors: Yang, Y. / Ko, T.P. / Liu, L. / Li, J. / Huang, C.H. / Chan, H.C. / Ren, F. / Jia, D. / Wang, A.H.-J. / Guo, R.T. / Chen, J. / Du, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wl7.cif.gz | 87.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wl7.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 3wl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wl/3wl7 ftp://data.pdbj.org/pub/pdb/validation_reports/wl/3wl7 | HTTPS FTP |
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-Related structure data
Related structure data | 3wl5SC 3wl6C 3wl8C 3wlaC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39328.789 Da / Num. of mol.: 1 / Fragment: UNP residues 30-379 / Mutation: S172C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: VM15C / Gene: pvaB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9LCQ7, beta-diketone hydrolase |
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#2: Chemical | ChemComp-P2D / |
#3: Chemical | ChemComp-CIT / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1M tri-sodium citrate, pH 5.6, 28% w/v Polyethylene Glycol 4000, 5% w/v n-Octyl-beta-D-glucoside, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 29, 2013 |
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→25 Å / Num. all: 38402 / Num. obs: 37918 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 7.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 41.7 |
Reflection shell | Resolution: 1.67→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 8 / Num. unique all: 3681 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3WL5 Resolution: 1.67→25 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 34.7034 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.77 Å2 / Biso mean: 17.1829 Å2 / Biso min: 7.59 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.67→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.67→1.73 Å
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