+Open data
-Basic information
Entry | Database: PDB / ID: 1r1d | ||||||
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Title | Structure of a Carboxylesterase from Bacillus stearothermophilus | ||||||
Components | Carboxylesterase | ||||||
Keywords | HYDROLASE / Structural genomics / MCSG / carboxylesterase / Bacillus stearothermophilus / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Cuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Structure of a Carboxylesterase from Bacillus stearothermophilus Authors: Cuff, M.E. / Zhou, M. / Collart, F. / Joachimiak, A. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1d.cif.gz | 122.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1d.ent.gz | 100.4 KB | Display | PDB format |
PDBx/mmJSON format | 1r1d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1d ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1d | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28859.406 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Gene: EST / Production host: Escherichia coli (E. coli) / References: UniProt: Q06174, carboxylesterase #2: Chemical | #3: 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: 3.14 Å3/Da / Density % sol: 60.78 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, PEG 3350, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å |
Detector | Type: CUSTOM-MADE / Detector: CCD / Date: Jul 2, 2003 / Details: SBC2 |
Radiation | Monochromator: sagitally focussed Si(111) / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→27.28 Å / Num. all: 53056 / Num. obs: 47271 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 20.5 Å2 / Limit h max: 34 / Limit h min: 0 / Limit k max: 42 / Limit k min: 0 / Limit l max: 68 / Limit l min: 0 / Observed criterion F max: 1935980.96 / Observed criterion F min: 9.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→27.28 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 52.5217 Å2 / ksol: 0.316936 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.1 Å2 / Biso mean: 37.58 Å2 / Biso min: 6.93 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→27.28 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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