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- PDB-7bfn: Apo form of Thermogutta terrifontis esterase 2 -

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Basic information

Entry
Database: PDB / ID: 7bfn
TitleApo form of Thermogutta terrifontis esterase 2
ComponentsEsterase
KeywordsHYDROLASE / nerve agent / conjugate / esterase
Function / homology: / BD-FAE / carboxylesterase / carboxylesterase activity / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Esterase / Putative lipase/esterase
Function and homology information
Biological speciesThermogutta terrifontis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)31,7112
Polymers31,6151
Non-polymers961
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area11970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.210, 67.700, 74.580
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: 31614.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermogutta terrifontis (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0X1KHD1, UniProt: A0A286RIX1*PLUS, carboxylesterase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.24 Å3/Da / Density % sol: 45.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 50 mM HEPES, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 4, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.19_4092refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ao9

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
RfactorNum. reflection% reflection
Rfree0.2641 1264 4.01 %
Rwork0.2307 30289 -
obs0.2321 31553 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2078 0 5 89 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00532151
X-RAY DIFFRACTIONf_angle_d0.8152914
X-RAY DIFFRACTIONf_chiral_restr0.0524306
X-RAY DIFFRACTIONf_plane_restr0.0091386
X-RAY DIFFRACTIONf_dihedral_angle_d5.6014296
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.49111330.44323200X-RAY DIFFRACTION95.36
1.77-1.850.41481380.39433293X-RAY DIFFRACTION98.82
1.85-1.950.33881390.33363329X-RAY DIFFRACTION98.66
1.95-2.070.30561380.29833320X-RAY DIFFRACTION98.29
2.07-2.230.31771400.29183332X-RAY DIFFRACTION98.64
2.23-2.450.30651410.27113390X-RAY DIFFRACTION99.27
2.45-2.810.29041420.25793392X-RAY DIFFRACTION99.58
2.81-3.540.27271430.2383447X-RAY DIFFRACTION99.69
3.54-33.850.21481500.17653586X-RAY DIFFRACTION99.71
Refinement TLS params.Method: refined / Origin x: 9.18774023826 Å / Origin y: 11.745845867 Å / Origin z: 14.8220519784 Å
111213212223313233
T0.334189202231 Å20.0224949408727 Å20.041844110684 Å2-0.35620572425 Å2-0.0162421676264 Å2--0.35815113881 Å2
L1.3846908403 °2-0.67154619055 °2-0.200419731299 °2-4.02711250196 °20.145258665021 °2--0.386202647821 °2
S0.089649122232 Å °0.0563424918925 Å °0.126358459284 Å °-0.154520596458 Å °0.0379004182413 Å °-0.403210267191 Å °0.0396558463605 Å °-0.0510120425109 Å °0.0145915638131 Å °
Refinement TLS groupSelection details: chain A

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