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- PDB-7bft: Thermogutta terrifontis esterase 2 phosphoramylated by tabun -

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Basic information

Entry
Database: PDB / ID: 7bft
TitleThermogutta terrifontis esterase 2 phosphoramylated by tabun
ComponentsEsterase
KeywordsHYDROLASE / nerve agent / conjugate / esterase
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity / triacylglycerol lipase activity
Similarity search - Function
: / BD-FAE / : / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
PHOSPHATE ION / Esterase / Putative lipase/esterase
Similarity search - Component
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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)31,8452
Polymers31,7501
Non-polymers951
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-9 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.740, 67.870, 74.940
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: 31750.066 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.15 Å3/Da / Density % sol: 42.85 %
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: 0.9801 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.99→43.67 Å / Num. obs: 19260 / % possible obs: 99.54 % / Redundancy: 12.9 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.998 / Net I/σ(I): 17.14
Reflection shellResolution: 1.99→2.064 Å / Num. unique obs: 1851 / CC1/2: 0.978

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Processing

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

7bfn


Resolution: 1.99→43.67 Å / SU ML: 0.1833 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.2519
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1933 962 5 %
Rwork0.1596 18271 -
obs0.1613 19233 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.09 Å2
Refinement stepCycle: LAST / Resolution: 1.99→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 5 231 2284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082141
X-RAY DIFFRACTIONf_angle_d1.05372908
X-RAY DIFFRACTIONf_chiral_restr0.0644306
X-RAY DIFFRACTIONf_plane_restr0.0089384
X-RAY DIFFRACTIONf_dihedral_angle_d6.3247301
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.10.22761330.17912501X-RAY DIFFRACTION97.81
2.1-2.230.21651340.16922568X-RAY DIFFRACTION99.52
2.23-2.40.22311360.16442584X-RAY DIFFRACTION99.85
2.4-2.640.20821370.16692588X-RAY DIFFRACTION99.89
2.64-3.030.21891380.17412617X-RAY DIFFRACTION99.93
3.03-3.810.18791390.15772642X-RAY DIFFRACTION99.96
3.81-43.670.16181450.14582771X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: 9.32749812341 Å / Origin y: 11.7099853358 Å / Origin z: 15.3418318029 Å
111213212223313233
T0.158505052823 Å20.0101490230254 Å2-0.0120301722418 Å2-0.157901788064 Å2-0.00739643147303 Å2--0.157241411053 Å2
L0.969114671665 °2-0.0652673177825 °20.0442922024879 °2-1.0494714496 °20.0235990243628 °2--0.659801750682 °2
S0.00681287484928 Å °0.0769951076331 Å °0.0227733333651 Å °0.113447922343 Å °0.0272131504979 Å °-0.127544070406 Å °0.0396525517608 Å °0.0626881355677 Å °-0.000290063149821 Å °
Refinement TLS groupSelection details: chain A

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