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Yorodumi- PDB-3s8y: Bromide soaked structure of an esterase from the oil-degrading ba... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s8y | ||||||
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Title | Bromide soaked structure of an esterase from the oil-degrading bacterium Oleispira antarctica | ||||||
Components | Esterase APC40077 | ||||||
Keywords | HYDROLASE / Rossmann fold | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Petit, P. / Dong, A. / Kagan, O. / Savchenko, A. / Yakunin, A.F. | ||||||
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 | 3s8y.cif.gz | 124.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s8y.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/3s8y ftp://data.pdbj.org/pub/pdb/validation_reports/s8/3s8y | HTTPS FTP |
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-Related structure data
Related structure data | 3i6ySC 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: 31065.502 Da / Num. of mol.: 1 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) / References: UniProt: D0VWZ4, arylesterase |
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#2: Chemical | ChemComp-BR / |
#3: 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: 2.66 Å3/Da / Density % sol: 53.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.4M Di-Ammonium citrate, 22% PEG3350, Soaking step: KBr 0.8M, 30s. , pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Apr 15, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.73 Å / Num. obs: 19720 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Rmerge(I) obs: 0.09 / Rsym value: 0.083 / Net I/σ(I): 17 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 6.3 / Num. unique all: 2775 / Rsym value: 0.27 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3I6Y Resolution: 2.1→19.69 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 15.75 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.681 Å2 / ksol: 0.406 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→19.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -4.8407 Å / Origin y: 15.6966 Å / Origin z: -7.7503 Å
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Refinement TLS group | Selection details: all |