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- PDB-8uqy: Round 18 Arylesterase Variant of Phosphotriesterase Bound to Euro... -

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Basic information

Entry
Database: PDB / ID: 8uqy
TitleRound 18 Arylesterase Variant of Phosphotriesterase Bound to Europium(III) Measured at 9.5 keV
ComponentsPhosphotriesterase variant PTE-R18
KeywordsHYDROLASE / Phosphotriesterase / 9.5 keV / Europium
Function / homology
Function and homology information


aryldialkylphosphatase / hydrolase activity, acting on ester bonds / 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
Similarity search - Domain/homology
EUROPIUM (III) ION / Parathion hydrolase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsBreeze, C.W. / Frkic, R.L. / Campbell, E.C. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: Mononuclear binding and catalytic activity of europium(III) and gadolinium(III) at the active site of the model metalloenzyme phosphotriesterase.
Authors: Breeze, C.W. / Nakano, Y. / Campbell, E.C. / Frkic, R.L. / Lupton, D.W. / Jackson, C.J.
History
DepositionOct 25, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotriesterase variant PTE-R18
B: Phosphotriesterase variant PTE-R18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1129
Polymers72,4172
Non-polymers6967
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-92 kcal/mol
Surface area22210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.511, 85.889, 89.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Phosphotriesterase variant PTE-R18


Mass: 36208.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A060GYS7
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-EU3 / EUROPIUM (III) ION


Mass: 151.964 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Eu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 100 mM Sodium cacodylate, 14% (v/v) MPD, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.305 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.305 Å / Relative weight: 1
ReflectionResolution: 1.78→44.67 Å / Num. obs: 63759 / % possible obs: 100 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.022 / Rrim(I) all: 0.111 / Χ2: 1.02 / Net I/σ(I): 18.7 / Num. measured all: 1673385
Reflection shellResolution: 1.78→1.82 Å / % possible obs: 100 % / Redundancy: 22.2 % / Rmerge(I) obs: 3.131 / Num. measured all: 79796 / Num. unique obs: 3593 / CC1/2: 0.655 / Rpim(I) all: 0.668 / Rrim(I) all: 3.204 / Χ2: 1.01 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→42.94 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2005 3227 5.07 %
Rwork0.1613 --
obs0.1633 63627 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→42.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4927 0 35 297 5259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d0.987
X-RAY DIFFRACTIONf_dihedral_angle_d10.132713
X-RAY DIFFRACTIONf_chiral_restr0.06802
X-RAY DIFFRACTIONf_plane_restr0.011881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.810.39271070.3552616X-RAY DIFFRACTION100
1.81-1.830.33641650.30162563X-RAY DIFFRACTION100
1.83-1.860.30781470.26752575X-RAY DIFFRACTION99
1.86-1.90.28211440.24572582X-RAY DIFFRACTION100
1.9-1.930.27581380.23692589X-RAY DIFFRACTION100
1.93-1.970.30211550.22272567X-RAY DIFFRACTION100
1.97-2.010.21991350.20572596X-RAY DIFFRACTION100
2.01-2.050.21261310.18812608X-RAY DIFFRACTION100
2.05-2.10.24961320.18672629X-RAY DIFFRACTION100
2.1-2.150.2251440.17432588X-RAY DIFFRACTION100
2.15-2.210.21671490.16422589X-RAY DIFFRACTION100
2.21-2.280.19931410.15852604X-RAY DIFFRACTION100
2.28-2.350.21521350.15992614X-RAY DIFFRACTION100
2.35-2.430.21721730.16262594X-RAY DIFFRACTION100
2.43-2.530.24151660.16152597X-RAY DIFFRACTION100
2.53-2.650.20271410.16732618X-RAY DIFFRACTION100
2.65-2.790.22941670.15322600X-RAY DIFFRACTION100
2.79-2.960.19981130.15562686X-RAY DIFFRACTION100
2.96-3.190.20481140.16362678X-RAY DIFFRACTION100
3.19-3.510.20841350.152628X-RAY DIFFRACTION100
3.51-4.020.17321370.13852702X-RAY DIFFRACTION100
4.02-5.060.1391150.12422740X-RAY DIFFRACTION100
5.06-42.940.1691430.16312837X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.4909 Å / Origin y: 22.8051 Å / Origin z: 22.0714 Å
111213212223313233
T0.1646 Å2-0.0158 Å2-0.0076 Å2-0.2784 Å20.0067 Å2--0.3205 Å2
L1.1894 °2-0.0664 °2-0.3929 °2-0.2885 °2-0.0123 °2--1.3634 °2
S0.0056 Å °-0.2753 Å °0.0236 Å °0.0008 Å °0.0116 Å °0.015 Å °-0.0407 Å °0.0182 Å °-0.0148 Å °
Refinement TLS groupSelection details: all

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