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Yorodumi- PDB-5gv5: Crystal structure of Candida antarctica Lipase B with active Ser1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gv5 | |||||||||
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Title | Crystal structure of Candida antarctica Lipase B with active Ser105 modified with a phosphonate inhibitor | |||||||||
Components | Lipase B | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Lipase / Inhibitor / Phosphonate / CAL-B / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | Function and homology information triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process Similarity search - Function | |||||||||
Biological species | Pseudozyma antarctica (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.89 Å | |||||||||
Authors | Park, S.Y. / Lee, H. | |||||||||
Citation | Journal: Acs Catalysis / Year: 2016 Title: Structural and Experimental Evidence for the Enantiomeric Recognition toward a Bulky sec-Alcohol by Candida antarctica Lipase B Authors: Park, K. / Kim, S. / Park, J. / Joe, S. / Min, B. / Oh, J. / Song, J. / Park, S.Y. / Park, S. / Lee, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gv5.cif.gz | 450.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gv5.ent.gz | 379.9 KB | Display | PDB format |
PDBx/mmJSON format | 5gv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gv5_validation.pdf.gz | 4.6 MB | Display | wwPDB validaton report |
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Full document | 5gv5_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 5gv5_validation.xml.gz | 88 KB | Display | |
Data in CIF | 5gv5_validation.cif.gz | 115.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/5gv5 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/5gv5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
-Components
#1: Protein | Mass: 33040.238 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudozyma antarctica (fungus) / Strain: T-34 / Production host: Aspergillus niger (mold) References: UniProt: P41365, UniProt: M9MDK9*PLUS, triacylglycerol lipase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Chemical | ChemComp-MSW / [( |
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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: 3.22 Å3/Da / Density % sol: 61.75 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 1.2 M Ammonium dihydrogen phosphate, Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 74402 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 2.9→2.95 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.432 / Mean I/σ(I) obs: 4.1 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Resolution: 2.89→30.63 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.556 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 36.049 Å2
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Refinement step | Cycle: LAST / Resolution: 2.89→30.63 Å
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Refine LS restraints |
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