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- PDB-8uqw: Round 18 Arylesterase Variant of Apo-Phosphotriesterase Measured ... -

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Basic information

Entry
Database: PDB / ID: 8uqw
TitleRound 18 Arylesterase Variant of Apo-Phosphotriesterase Measured at 13 keV
ComponentsPhosphotriesterase variant PTE-R18
KeywordsHYDROLASE / Apo-Phosphotriesterase / 13 keV
Function / homology
Function and homology information


aryldialkylphosphatase / hydrolase activity, acting on ester bonds / catabolic process / zinc ion binding
Similarity search - Function
Aryldialkylphosphatase, zinc-binding site / Phosphotriesterase family signature 1. / Phosphotriesterase / Phosphotriesterase family / Phosphotriesterase family profile. / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)72,7246
Polymers72,4172
Non-polymers3074
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-59 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.630, 86.215, 89.160
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.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
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: 0.9537 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: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→44.58 Å / Num. obs: 105750 / % possible obs: 99.7 % / Redundancy: 40.6 % / CC1/2: 1 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.021 / Rrim(I) all: 0.134 / Χ2: 1.08 / Net I/σ(I): 14.2 / Num. measured all: 4295366
Reflection shellResolution: 1.5→1.53 Å / % possible obs: 99.1 % / Redundancy: 41.1 % / Rmerge(I) obs: 4.314 / Num. measured all: 212320 / Num. unique obs: 5167 / CC1/2: 0.665 / Rpim(I) all: 0.673 / Rrim(I) all: 4.367 / Χ2: 1.3 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.6 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2061 5212 4.94 %
Rwork0.1837 --
obs0.1848 105582 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→39.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 18 385 5290
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.182
X-RAY DIFFRACTIONf_dihedral_angle_d10.551714
X-RAY DIFFRACTIONf_chiral_restr0.061801
X-RAY DIFFRACTIONf_plane_restr0.014883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33551820.32893263X-RAY DIFFRACTION98
1.52-1.530.34581860.313259X-RAY DIFFRACTION99
1.53-1.550.34891840.30943289X-RAY DIFFRACTION99
1.55-1.570.28841570.30173285X-RAY DIFFRACTION99
1.57-1.590.37621600.30983301X-RAY DIFFRACTION99
1.59-1.620.32321730.30013302X-RAY DIFFRACTION99
1.62-1.640.31351590.28673333X-RAY DIFFRACTION99
1.64-1.660.28411510.26793300X-RAY DIFFRACTION99
1.66-1.690.25051500.2543345X-RAY DIFFRACTION99
1.69-1.720.27811490.24663324X-RAY DIFFRACTION99
1.72-1.750.26741650.24053308X-RAY DIFFRACTION99
1.75-1.780.25481330.233353X-RAY DIFFRACTION100
1.78-1.810.2651430.22713363X-RAY DIFFRACTION100
1.81-1.850.25031800.2263305X-RAY DIFFRACTION100
1.85-1.890.2731970.21753283X-RAY DIFFRACTION100
1.89-1.930.22771810.22173336X-RAY DIFFRACTION100
1.93-1.980.25711850.22013338X-RAY DIFFRACTION100
1.98-2.040.25321950.20323329X-RAY DIFFRACTION100
2.04-2.10.23171850.19783333X-RAY DIFFRACTION100
2.1-2.160.23252060.18873297X-RAY DIFFRACTION100
2.16-2.240.22792020.18253323X-RAY DIFFRACTION100
2.24-2.330.20881920.17763361X-RAY DIFFRACTION100
2.33-2.440.22361720.1753361X-RAY DIFFRACTION100
2.44-2.560.18862020.17483334X-RAY DIFFRACTION100
2.56-2.730.19641410.17993409X-RAY DIFFRACTION100
2.73-2.940.18771490.17063425X-RAY DIFFRACTION100
2.94-3.230.18672050.17023379X-RAY DIFFRACTION100
3.23-3.70.19461620.16143455X-RAY DIFFRACTION100
3.7-4.660.16971240.13893508X-RAY DIFFRACTION100
4.66-39.60.15332420.16343569X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.3479 Å / Origin y: 22.7313 Å / Origin z: 21.842 Å
111213212223313233
T0.1646 Å2-0.014 Å2-0.0055 Å2-0.2159 Å20.0035 Å2--0.2082 Å2
L1.7676 °2-0.1101 °2-0.386 °2-0.3542 °2-0.0223 °2--1.0592 °2
S0.0096 Å °-0.4254 Å °0.0383 Å °-0.0033 Å °0.0125 Å °0.0057 Å °-0.0281 Å °0.054 Å °-0.0194 Å °
Refinement TLS groupSelection details: all

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