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- PDB-7bfu: Thermogutta terrifontis esterase 2 phosphonylated by sarin -

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Basic information

Entry
Database: PDB / ID: 7bfu
TitleThermogutta terrifontis esterase 2 phosphonylated by sarin
ComponentsEsterase
KeywordsHYDROLASE / nerve agent / conjugate / esterase
Function / homology
Function and homology information


carboxylesterase / lipase activity / carboxylesterase activity
Similarity search - Function
: / BD-FAE / : / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
ETHANOL / Esterase / Putative lipase/esterase
Similarity search - Component
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrazzolotto, X.B. / Bzdrenga, J. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-4210 France
CitationJournal: 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
DepositionJan 4, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7812
Polymers31,7351
Non-polymers461
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint3 kcal/mol
Surface area11860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.860, 67.710, 75.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Esterase / Esterase Est2


Mass: 31735.051 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
#2: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.65→43.34 Å / Num. obs: 32804 / % possible obs: 98.07 % / Redundancy: 11.4 % / Biso Wilson estimate: 26.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.4
Reflection shellResolution: 1.65→1.709 Å / Num. unique obs: 3175 / CC1/2: 0.641

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19_4092refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7bfn

7bfn


Resolution: 1.65→43.34 Å / SU ML: 0.3244 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.9556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1310 4 %
Rwork0.1784 31418 -
obs0.18 32728 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2156 0 3 271 2430
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752252
X-RAY DIFFRACTIONf_angle_d1.01023058
X-RAY DIFFRACTIONf_chiral_restr0.0624319
X-RAY DIFFRACTIONf_plane_restr0.0086406
X-RAY DIFFRACTIONf_dihedral_angle_d6.761315
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.47981400.48353356X-RAY DIFFRACTION96.63
1.72-1.790.47151430.37583419X-RAY DIFFRACTION97.11
1.79-1.890.31131420.27493412X-RAY DIFFRACTION97.05
1.89-2.010.25781430.2163435X-RAY DIFFRACTION97.63
2.01-2.160.26661440.19813464X-RAY DIFFRACTION98.07
2.16-2.380.2141460.16123491X-RAY DIFFRACTION98.64
2.38-2.720.1951470.16213525X-RAY DIFFRACTION98.71
2.72-3.430.21131480.16833569X-RAY DIFFRACTION99.15
3.43-43.340.17421570.14053747X-RAY DIFFRACTION99.62
Refinement TLS params.Method: refined / Origin x: 9.16019378836 Å / Origin y: 11.056546923 Å / Origin z: 14.6520619566 Å
111213212223313233
T0.16511891736 Å20.00812964267525 Å2-0.00909485044655 Å2-0.172100424295 Å2-0.00127600873837 Å2--0.167162628114 Å2
L0.811214367011 °20.0468922467511 °2-0.336856356835 °2-1.12918172321 °2-0.0925190911355 °2--0.792829341879 °2
S-0.00758142119526 Å °0.0444327448778 Å °-0.0156461835179 Å °0.0579970030492 Å °-0.00277397061444 Å °-0.0881466778052 Å °0.0622356004152 Å °0.0217642217688 Å °-5.49227628762E-6 Å °
Refinement TLS groupSelection details: chain A

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