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- PDB-8sfm: Crystal structure of the engineered SsoPox variant IVB10 in alter... -

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Basic information

Entry
Database: PDB / ID: 8sfm
TitleCrystal structure of the engineered SsoPox variant IVB10 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
: / : / PHOSPHATE ION / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 11, 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

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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)35,9717
Polymers35,5151
Non-polymers4566
Water3,639202
1
D: Aryldialkylphosphatase
hetero molecules

D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,94214
Polymers71,0302
Non-polymers91212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area5400 Å2
ΔGint-100 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.110, 74.610, 137.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules D

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


Mass: 35514.789 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: IVB10
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 6 types, 208 molecules

#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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.42 %
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: 1.5→68.85 Å / Num. obs: 101746 / % possible obs: 99.6 % / Redundancy: 3.72 % / CC1/2: 0.997 / Rrim(I) all: 0.069 / Net I/σ(I): 11.5
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.77 % / Num. unique obs: 17921 / CC1/2: 0.874 / Rrim(I) all: 0.461

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→39.72 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 23.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 5105 5.02 %RANDOM
Rwork0.2008 ---
obs0.2023 101736 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 0 202 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072523
X-RAY DIFFRACTIONf_angle_d0.9213411
X-RAY DIFFRACTIONf_dihedral_angle_d7.627348
X-RAY DIFFRACTIONf_chiral_restr0.066379
X-RAY DIFFRACTIONf_plane_restr0.007445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.33011720.30493209X-RAY DIFFRACTION100
1.52-1.530.28381720.27953281X-RAY DIFFRACTION100
1.53-1.550.27831720.26963206X-RAY DIFFRACTION100
1.55-1.570.28511690.25083180X-RAY DIFFRACTION100
1.57-1.590.31361730.2533250X-RAY DIFFRACTION99
1.59-1.620.27661700.2433196X-RAY DIFFRACTION99
1.62-1.640.23951770.2413278X-RAY DIFFRACTION100
1.64-1.660.24671670.23393171X-RAY DIFFRACTION100
1.66-1.690.23221730.2363261X-RAY DIFFRACTION100
1.69-1.720.23211690.23473185X-RAY DIFFRACTION100
1.72-1.750.25031720.25133261X-RAY DIFFRACTION100
1.75-1.780.29961670.23423230X-RAY DIFFRACTION100
1.78-1.810.24291710.21823213X-RAY DIFFRACTION100
1.81-1.850.25021680.21353240X-RAY DIFFRACTION100
1.85-1.890.25931690.2033247X-RAY DIFFRACTION100
1.89-1.930.27481720.2093202X-RAY DIFFRACTION100
1.93-1.980.23131720.20873248X-RAY DIFFRACTION100
1.98-2.040.23741720.2133207X-RAY DIFFRACTION100
2.04-2.10.22561660.20263193X-RAY DIFFRACTION100
2.1-2.160.25161700.19933229X-RAY DIFFRACTION99
2.16-2.240.24761700.19773265X-RAY DIFFRACTION99
2.24-2.330.22761680.19763201X-RAY DIFFRACTION99
2.33-2.440.24331690.20773206X-RAY DIFFRACTION100
2.44-2.560.23041680.19843237X-RAY DIFFRACTION99
2.56-2.730.24661690.20953193X-RAY DIFFRACTION99
2.73-2.940.22331730.20363201X-RAY DIFFRACTION100
2.94-3.230.22571730.19183230X-RAY DIFFRACTION100
3.23-3.70.19751680.18953193X-RAY DIFFRACTION99
3.7-4.660.2011600.16233208X-RAY DIFFRACTION99
4.66-39.720.21311740.19183210X-RAY DIFFRACTION99

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