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- PDB-7p85: Engineered phosphotriesterase BdPTE 10-2-C3(C59V/C227V) in comple... -

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Basic information

Entry
Database: PDB / ID: 7p85
TitleEngineered phosphotriesterase BdPTE 10-2-C3(C59V/C227V) in complex with ethyl-4-methylbenzylphosphonate
ComponentsParathion hydrolase
KeywordsHYDROLASE / BIOSCAVENGER / ENZYME ENGINEERING / ORGANOPHOSPHATE HYDROLASE / ORGANOPHOSPHOROUS COMPOUND / PHOSPHOTRIESTERASE
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / catabolic process / zinc ion binding / plasma membrane
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
ethyl-4-methylbenzylphosphonate / FORMIC ACID / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsEichinger, A. / Skerra, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other governmentBundesamt fuer Ausruestung, Informationstechnik und Nutzung der Bundeswehr, E/U2AD/GD003/GF560 Germany
CitationJournal: Biochemistry / Year: 2023
Title: Structural and Functional Analysis of a Highly Active Designed Phosphotriesterase for the Detoxification of Organophosphate Nerve Agents Reveals an Unpredicted Conformation of the Active Site Loop.
Authors: Job, L. / Kohler, A. / Eichinger, A. / Testanera, M. / Escher, B. / Worek, F. / Skerra, A.
History
DepositionJul 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 1, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,64011
Polymers37,6841
Non-polymers95610
Water4,522251
1
A: Parathion hydrolase
hetero molecules

A: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,28022
Polymers75,3692
Non-polymers1,91120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area5640 Å2
ΔGint-83 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.298, 69.298, 186.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Parathion hydrolase / Phosphotriesterase / PTE


Mass: 37684.441 Da / Num. of mol.: 1
Mutation: C59V, K77A, A80M, R118E, F132E, T173N, K185R, A203D, S222D, C227V, D233G, S238D, H254G, A270S, L271W, I274N, M293V, Y309W, R319S, P342S, G348T, T352E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Gene: opd / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P0A434, aryldialkylphosphatase

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Non-polymers , 6 types, 261 molecules

#2: Chemical ChemComp-5ZG / ethyl-4-methylbenzylphosphonate


Mass: 214.198 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15O3P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3 / Details: ammonium sulfate, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 27, 2019 / Details: Si mirror
RadiationMonochromator: Si 111 double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.467→64.977 Å / Num. all: 78996 / Num. obs: 78996 / % possible obs: 100 % / Redundancy: 22.5 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.201 / Rsym value: 0.196 / Net I/av σ(I): 1.8 / Net I/σ(I): 10.2 / Num. measured all: 1773620
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.47-1.5523.30.9640.8264395113640.2010.9850.9643.7100
1.55-1.6421.90.7591234942107320.1640.7770.7594.5100
1.64-1.7521.70.5821.2219427101160.1260.5960.5825.8100
1.75-1.8924.50.431.523202594620.0870.4390.438.3100
1.89-2.0723.40.295220424587280.0620.3020.29511.1100
2.07-2.32200.2032.815934979520.0460.2090.20313.1100
2.32-2.6822.10.1643.115586970560.0350.1680.16415.7100
2.68-3.2823.50.1363.414137960260.0280.1390.13618.5100
3.28-4.6419.70.1173.59376547510.0270.1210.11719.4100
4.64-49.00124.30.14236822428090.0290.1450.1422199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.18 Å49 Å
Translation6.18 Å49 Å

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Processing

Software
NameVersionClassification
MOSFLM7.2.2data reduction
SCALA3.3.22data scaling
PHASER2.8.2phasing
REFMAC5.8.0266refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PSC

1psc


Resolution: 1.47→49.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.683 / SU ML: 0.034 / SU R Cruickshank DPI: 0.0504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 3863 4.9 %RANDOM
Rwork0.1573 ---
obs0.1581 75013 99.99 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.07 Å2 / Biso mean: 17.411 Å2 / Biso min: 8.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0 Å2
2--0.06 Å2-0 Å2
3----0.12 Å2
Refinement stepCycle: final / Resolution: 1.47→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2556 0 52 251 2859
Biso mean--25.28 26.54 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132720
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172606
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.6363706
X-RAY DIFFRACTIONr_angle_other_deg0.5011.5735972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.43320.272147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7631528
X-RAY DIFFRACTIONr_chiral_restr0.0880.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02651
LS refinement shellResolution: 1.47→1.505 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 270 -
Rwork-5490 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 11.718 Å / Origin y: -33.493 Å / Origin z: -10.048 Å
111213212223313233
T0.0475 Å20.0058 Å2-0.0058 Å2-0.0255 Å20.0119 Å2--0.0214 Å2
L0.1178 °2-0.179 °20.0406 °2-0.3447 °2-0.1893 °2--0.3425 °2
S-0.0229 Å °-0.0309 Å °-0.0096 Å °0.014 Å °0.0584 Å °0.0252 Å °-0.0317 Å °-0.0374 Å °-0.0355 Å °

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