+Open data
-Basic information
Entry | Database: PDB / ID: 7bfv | ||||||
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Title | Thermogutta terrifontis esterase 2 phosphonylated by cyclosarin | ||||||
Components | Esterase | ||||||
Keywords | HYDROLASE / nerve agent / conjugate / esterase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Thermogutta terrifontis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å | ||||||
Authors | Brazzolotto, X.B. / Bzdrenga, J. / Nachon, F. | ||||||
Funding support | France, 1items
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Citation | Journal: Molecules / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bfv.cif.gz | 146.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bfv.ent.gz | 94 KB | Display | PDB format |
PDBx/mmJSON format | 7bfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/7bfv ftp://data.pdbj.org/pub/pdb/validation_reports/bf/7bfv | HTTPS FTP |
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-Related structure data
Related structure data | 7bfnSC 7bfoC 7bfrC 7bftC 7bfuC 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: 31775.113 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A0A0X1KHD1, UniProt: A0A286RIX1*PLUS, carboxylesterase |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.53 % |
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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: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 4, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 1.84→33.87 Å / Num. obs: 25095 / % possible obs: 99.26 % / Redundancy: 13 % / Biso Wilson estimate: 33.92 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.16 |
Reflection shell | Resolution: 1.84→1.906 Å / Num. unique obs: 2435 / CC1/2: 0.99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7bfn Resolution: 1.84→33.87 Å / SU ML: 0.2248 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.2281 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: 52.22 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→33.87 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: 9.58597996737 Å / Origin y: 11.9186115593 Å / Origin z: 15.3972875121 Å
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Refinement TLS group | Selection details: chain A |