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Yorodumi- PDB-3i6y: Structure of an esterase from the oil-degrading bacterium Oleispi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i6y | ||||||
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Title | Structure of an esterase from the oil-degrading bacterium Oleispira antarctica | ||||||
Components | Esterase APC40077 | ||||||
Keywords | HYDROLASE / Oleispira antarctica / lipase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information S-formylglutathione hydrolase / S-formylglutathione hydrolase activity / formaldehyde catabolic process / carboxylic ester hydrolase activity Similarity search - Function | ||||||
Biological species | Oleispira antarctica (bacteria) | ||||||
Method | X-RAY DIFFRACTION / PHASER / Resolution: 1.75 Å | ||||||
Authors | Singer, A.U. / Evdokimova, E. / Kagan, O. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: Biochem.J. / Year: 2012 Title: Structure and activity of the cold-active and anion-activated carboxyl esterase OLEI01171 from the oil-degrading marine bacterium Oleispira antarctica. Authors: Lemak, S. / Tchigvintsev, A. / Petit, P. / Flick, R. / Singer, A.U. / Brown, G. / Evdokimova, E. / Egorova, O. / Gonzalez, C.F. / Chernikova, T.N. / Yakimov, M.M. / Kube, M. / Reinhardt, R. ...Authors: Lemak, S. / Tchigvintsev, A. / Petit, P. / Flick, R. / Singer, A.U. / Brown, G. / Evdokimova, E. / Egorova, O. / Gonzalez, C.F. / Chernikova, T.N. / Yakimov, M.M. / Kube, M. / Reinhardt, R. / Golyshin, P.N. / Savchenko, A. / Yakunin, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i6y.cif.gz | 137.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i6y.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 3i6y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3i6y_validation.pdf.gz | 462.8 KB | Display | wwPDB validaton report |
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Full document | 3i6y_full_validation.pdf.gz | 474.4 KB | Display | |
Data in XML | 3i6y_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 3i6y_validation.cif.gz | 42.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i6/3i6y ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i6y | HTTPS FTP |
-Related structure data
Related structure data | 3s8yC 1pv1S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31393.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: thrombin cleavage / Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: olei01171 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: D0VWZ4*PLUS, arylesterase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
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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: 2.64 Å3/Da / Density % sol: 53.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.2 M diammonium hydrogen citrate, 20% PEG 3350, Cryoprotected in Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 294K, pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 23, 2009 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.94 Å / Num. all: 71147 / Num. obs: 61811 / % possible obs: 86.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.338 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 5.8 / Num. unique all: 4596 / % possible all: 64.8 |
-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB entry 1PV1 Resolution: 1.75→27.94 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.138 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / 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: 15.966 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→27.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.793 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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