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- PDB-8uqz: Round 18 Arylesterase Variant of Phosphotriesterase Bound to Gado... -

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Basic information

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


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
GADOLINIUM ION / Phosphotriesterase variant PTE-R18
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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)73,1189
Polymers72,4172
Non-polymers7017
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-93 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.714, 86.138, 89.247
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-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Gd / 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.: 334 / 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: 45.93 %
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: 1.3051 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: 1.3051 Å / Relative weight: 1
ReflectionResolution: 1.61→44.62 Å / Num. obs: 84562 / % possible obs: 98.3 % / Redundancy: 40 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.021 / Rrim(I) all: 0.133 / Χ2: 1.03 / Net I/σ(I): 21.2 / Num. measured all: 3380001
Reflection shellResolution: 1.61→1.64 Å / % possible obs: 94.4 % / Redundancy: 36.5 % / Rmerge(I) obs: 4.232 / Num. measured all: 145095 / Num. unique obs: 3978 / CC1/2: 0.662 / Rpim(I) all: 0.698 / Rrim(I) all: 4.291 / Χ2: 1.03 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→42.86 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1951 3960 4.69 %
Rwork0.1704 --
obs0.1716 84469 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.61→42.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 35 334 5313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.928
X-RAY DIFFRACTIONf_dihedral_angle_d11.957716
X-RAY DIFFRACTIONf_chiral_restr0.054804
X-RAY DIFFRACTIONf_plane_restr0.01884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.630.4565990.37572765X-RAY DIFFRACTION94
1.63-1.650.31531050.33832806X-RAY DIFFRACTION95
1.65-1.670.32511190.30332802X-RAY DIFFRACTION97
1.67-1.690.33121590.27652771X-RAY DIFFRACTION97
1.69-1.720.29521570.25832781X-RAY DIFFRACTION97
1.72-1.740.29051550.24352797X-RAY DIFFRACTION97
1.74-1.770.2781640.22362798X-RAY DIFFRACTION97
1.77-1.80.21811450.22132802X-RAY DIFFRACTION97
1.8-1.830.25881480.22322824X-RAY DIFFRACTION97
1.83-1.870.22551230.22112848X-RAY DIFFRACTION98
1.87-1.90.2941300.22062854X-RAY DIFFRACTION98
1.9-1.940.30981560.2152836X-RAY DIFFRACTION98
1.94-1.980.23021370.20372846X-RAY DIFFRACTION98
1.98-2.030.22771570.19262840X-RAY DIFFRACTION98
2.03-2.080.211530.18082843X-RAY DIFFRACTION98
2.08-2.140.20491160.17122919X-RAY DIFFRACTION99
2.14-2.20.18621490.16822859X-RAY DIFFRACTION99
2.2-2.270.19641520.15962868X-RAY DIFFRACTION99
2.27-2.350.18251450.16582885X-RAY DIFFRACTION99
2.35-2.440.18051730.1642878X-RAY DIFFRACTION99
2.44-2.560.20041700.15962883X-RAY DIFFRACTION99
2.56-2.690.17911210.16342963X-RAY DIFFRACTION100
2.69-2.860.17561300.16132932X-RAY DIFFRACTION99
2.86-3.080.2031380.172957X-RAY DIFFRACTION99
3.08-3.390.19361410.16282936X-RAY DIFFRACTION100
3.39-3.880.15361510.15023008X-RAY DIFFRACTION100
3.88-4.890.16091300.12873023X-RAY DIFFRACTION100
4.89-42.860.16251370.16163185X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 15.5524 Å / Origin y: 22.8493 Å / Origin z: 21.8618 Å
111213212223313233
T0.1497 Å2-0.0107 Å2-0.0062 Å2-0.1872 Å20.0046 Å2--0.258 Å2
L1.2344 °2-0.0659 °2-0.3953 °2-0.2955 °2-0.0202 °2--1.2427 °2
S0.0017 Å °-0.2857 Å °0.0187 Å °-0.0305 Å °0.012 Å °0.0098 Å °-0.0276 Å °0.0179 Å °-0.0084 Å °
Refinement TLS groupSelection details: all

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