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Open data
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Basic information
Entry | Database: PDB / ID: 7bfn | ||||||
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Title | Apo form of Thermogutta terrifontis esterase 2 | ||||||
![]() | Esterase | ||||||
![]() | HYDROLASE / nerve agent / conjugate / esterase | ||||||
Function / homology | : / BD-FAE / carboxylesterase / lipase activity / carboxylesterase activity / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / Esterase / Putative lipase/esterase![]() | ||||||
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 | ![]() | 142.9 KB | Display | ![]() |
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PDB format | ![]() | 93.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.2 KB | Display | ![]() |
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Full document | ![]() | 448.1 KB | Display | |
Data in XML | ![]() | 12.9 KB | Display | |
Data in CIF | ![]() | 17.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bfoC ![]() 7bfrC ![]() 7bftC ![]() 7bfuC ![]() 7bfvC ![]() 5ao9S 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: 31614.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A0X1KHD1, UniProt: A0A286RIX1*PLUS, carboxylesterase |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.7→33.85 Å / Num. obs: 31810 / % possible obs: 98.66 % / Redundancy: 12.8 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.71 |
Reflection shell | Resolution: 1.7→1.761 Å / Redundancy: 9.5 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 2990 / CC1/2: 0.776 / % possible all: 94.94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5ao9 Resolution: 1.7→33.85 Å / SU ML: 0.2694 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.8138 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: 65.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→33.85 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: 9.18774023826 Å / Origin y: 11.745845867 Å / Origin z: 14.8220519784 Å
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Refinement TLS group | Selection details: chain A |