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Yorodumi- PDB-3doi: Crystal Structure of a Thermostable Esterase complex with paraoxon -
+Open data
-Basic information
Entry | Database: PDB / ID: 3doi | ||||||
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Title | Crystal Structure of a Thermostable Esterase complex with paraoxon | ||||||
Components | esterase | ||||||
Keywords | HYDROLASE / alpha-beta Hydrolase / beta sheet | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Levisson, M. / Sun, L. / Hendriks, S. / Dijkstra, B.W. / Van der Oost, J. / Kengen, S.W.M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain. Authors: Levisson, M. / Sun, L. / Hendriks, S. / Swinkels, P. / Akveld, T. / Bultema, J.B. / Barendregt, A. / van den Heuvel, R.H.H. / Dijkstra, B.W. / van der Oost, J. / Kengen, S.W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3doi.cif.gz | 157.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3doi.ent.gz | 125.6 KB | Display | PDB format |
PDBx/mmJSON format | 3doi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/3doi ftp://data.pdbj.org/pub/pdb/validation_reports/do/3doi | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 43067.750 Da / Num. of mol.: 2 / Fragment: residues 17-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0033 / Plasmid: pET-24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WXP0, carboxylesterase #2: Chemical | |
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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: 2.9 Å3/Da / Density % sol: 57.57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG 8000, 1M lithium sulphate monohydrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2007 / Details: mirrors |
Radiation | Monochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 20405 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→37.69 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.894 / SU B: 20.655 / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.551 Å2
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Refinement step | Cycle: LAST / Resolution: 3→37.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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