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Yorodumi- PDB-2ogt: Crystal Structure of the Geobacillus Stearothermophilus Carboxyle... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ogt | ||||||
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Title | Crystal Structure of the Geobacillus Stearothermophilus Carboxylesterase EST55 at pH 6.8 | ||||||
Components | Thermostable carboxylesterase Est50 | ||||||
Keywords | HYDROLASE / CARBOXYLESTERASE / ALPHA/BETA HYDROLASE | ||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity Similarity search - Function | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Liu, P. / Ewis, H.E. / Tai, P.C. / Lu, C.D. / Weber, I.T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Crystal Structure of the Geobacillus stearothermophilus Carboxylesterase Est55 and Its Activation of Prodrug CPT-11. Authors: Liu, P. / Ewis, H.E. / Tai, P.C. / Lu, C.D. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ogt.cif.gz | 204.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ogt.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ogt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/2ogt ftp://data.pdbj.org/pub/pdb/validation_reports/og/2ogt | HTTPS FTP |
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-Related structure data
Related structure data | 2ogsC 1qe3S C: citing same article (ref.) S: Starting model for refinement |
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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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Details | Each asymmetric unit has one biological unit |
-Components
#1: Protein | Mass: 54925.082 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Production host: Escherichia coli (E. coli) / Strain (production host): Top 10 / References: UniProt: Q8GCC7, carboxylesterase | ||
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#2: Chemical | ChemComp-IOD / | ||
#3: Chemical | #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: 2.14 Å3/Da / Density % sol: 46.88 % |
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Crystal grow | pH: 6.8 Details: PEG3350,POTASSIUM IODINE, PH 6.8, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2003 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→50 Å / Num. obs: 68569 / % possible obs: 97.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.58→1.63 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.8 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1QE3 Resolution: 1.58→10 Å / Num. parameters: 34904 / Num. restraintsaints: 45343 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 22 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3771.34 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.58→10 Å
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Refine LS restraints |
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