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- PDB-8sfc: Crystal structure of the engineered SsoPox variant IVA4 in altern... -

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Basic information

Entry
Database: PDB / ID: 8sfc
TitleCrystal structure of the engineered SsoPox variant IVA4 in alternate state
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / Lactonase / quorum sensing / phosphotriesterase / arylesterase
Function / homology
Function and homology information


aryldialkylphosphatase activity / aryldialkylphosphatase / 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
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Daude, D. / Elias, M.H.
Funding support France, United States, 5items
OrganizationGrant numberCountry
Other governmentDGA France
Agence Nationale de la Recherche (ANR)10-IAHU-03 France
Other governmentMndrive United States
Other governmentBiotechnology Institute United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133487 United States
CitationJournal: Jacs Au / Year: 2024
Title: Changes in Active Site Loop Conformation Relate to the Transition toward a Novel Enzymatic Activity.
Authors: Jacquet, P. / Billot, R. / Shimon, A. / Hoekstra, N. / Bergonzi, C. / Jenks, A. / Chabriere, E. / Daude, D. / Elias, M.H.
History
DepositionApr 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7194
Polymers35,5121
Non-polymers2073
Water3,423190
1
D: Aryldialkylphosphatase
hetero molecules

D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4378
Polymers71,0242
Non-polymers4146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area3860 Å2
ΔGint-50 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.090, 74.950, 137.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aryldialkylphosphatase / Paraoxonase / SsoPox / Phosphotriesterase-like lactonase


Mass: 35511.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: php, SSO2522 / Variant: IVA4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q97VT7, aryldialkylphosphatase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (w/v) PEG 8000 and Tris-HCl buffer (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.774901 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.774901 Å / Relative weight: 1
ReflectionResolution: 1.4→68.56 Å / Num. obs: 124395 / % possible obs: 98.9 % / Redundancy: 3.36 % / CC1/2: 0.999 / Rrim(I) all: 0.044 / Net I/σ(I): 15.22
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.682 / Num. unique obs: 23305 / CC1/2: 0.83

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→37.48 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.17 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 3833 3.08 %RANDOM
Rwork0.2048 ---
obs0.2055 124350 98.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 190 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072484
X-RAY DIFFRACTIONf_angle_d0.8713363
X-RAY DIFFRACTIONf_dihedral_angle_d7.126343
X-RAY DIFFRACTIONf_chiral_restr0.075375
X-RAY DIFFRACTIONf_plane_restr0.007441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.40161430.37294534X-RAY DIFFRACTION100
1.42-1.440.38461410.35084402X-RAY DIFFRACTION99
1.44-1.460.35161470.32264557X-RAY DIFFRACTION98
1.46-1.480.32211360.30814324X-RAY DIFFRACTION98
1.48-1.50.29911460.2834575X-RAY DIFFRACTION100
1.5-1.520.3391390.27844397X-RAY DIFFRACTION99
1.52-1.550.29111440.28344462X-RAY DIFFRACTION99
1.55-1.570.27111410.26784441X-RAY DIFFRACTION99
1.57-1.60.28351430.25994537X-RAY DIFFRACTION100
1.6-1.630.27071430.25964469X-RAY DIFFRACTION100
1.63-1.670.291430.2514509X-RAY DIFFRACTION100
1.67-1.70.28931440.23574514X-RAY DIFFRACTION100
1.7-1.740.21621420.23154453X-RAY DIFFRACTION99
1.74-1.790.26861460.23184493X-RAY DIFFRACTION99
1.79-1.830.20711430.22464505X-RAY DIFFRACTION100
1.83-1.890.24871430.22224449X-RAY DIFFRACTION99
1.89-1.950.24061400.23094344X-RAY DIFFRACTION97
1.95-2.020.24681430.21364506X-RAY DIFFRACTION99
2.02-2.10.17491340.20824360X-RAY DIFFRACTION98
2.1-2.20.21391400.19834505X-RAY DIFFRACTION99
2.2-2.310.23141460.20274421X-RAY DIFFRACTION98
2.31-2.460.20541440.2084509X-RAY DIFFRACTION99
2.46-2.650.21171420.20244470X-RAY DIFFRACTION99
2.65-2.910.21631420.20354503X-RAY DIFFRACTION99
2.91-3.330.20061380.18944402X-RAY DIFFRACTION98
3.33-4.20.22771350.17494442X-RAY DIFFRACTION98
4.2-37.480.20291450.17384434X-RAY DIFFRACTION98

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