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Open data
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Basic information
Entry | Database: PDB / ID: 7bfr | ||||||
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Title | Thermogutta terrifontis esterase 2 phosphorylated by paraoxon | ||||||
![]() | Esterase![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Brazzolotto, X.B. / Bzdrenga, J. / Nachon, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Thermophilic Bacterial Esterase for Scavenging Nerve Agents: A Kinetic, Biophysical and Structural Study. Authors: Bzdrenga, J. / Trenet, E. / Chantegreil, F. / Bernal, K. / Nachon, F. / Brazzolotto, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.7 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7bfnSC ![]() 7bfoC ![]() 7bftC ![]() 7bfuC ![]() 7bfvC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 31722.996 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A0X1KHD1, UniProt: A0A286RIX1*PLUS, ![]() |
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#2: Chemical | ChemComp-CO3 / ![]() |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.44 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES pH 7.5, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.99→36.74 Å / Num. obs: 19251 / % possible obs: 98.59 % / Redundancy: 12.9 % / Biso Wilson estimate: 25.45 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.16 |
Reflection shell | Resolution: 1.99→2.061 Å / Num. unique obs: 1664 / CC1/2: 0.991 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 7bfn Resolution: 1.99→36.74 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.7007 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.99→36.74 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: 9.38340896778 Å / Origin y: 11.7106874529 Å / Origin z: 15.9283899174 Å
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Refinement TLS group | Selection details: chain A |