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- PDB-8sfa: Crystal structure of the engineered SsoPox variant IIIC1 -

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Basic information

Entry
Database: PDB / ID: 8sfa
TitleCrystal structure of the engineered SsoPox variant IIIC1
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: 2.32 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
S: Aryldialkylphosphatase
b: Aryldialkylphosphatase
t: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,52612
Polymers142,0674
Non-polymers4598
Water3,279182
1
D: Aryldialkylphosphatase
S: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2636
Polymers71,0342
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-68 kcal/mol
Surface area23660 Å2
MethodPISA
2
b: Aryldialkylphosphatase
t: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2636
Polymers71,0342
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-69 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.230, 104.290, 153.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35516.758 Da / Num. of mol.: 4
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: IIIC1
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.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.55 Å3/Da / Density % sol: 51.69 %
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: 1.033202 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033202 Å / Relative weight: 1
ReflectionResolution: 2.32→68.236 Å / Num. obs: 62986 / % possible obs: 99.2 % / Redundancy: 8.05 % / CC1/2: 0.999 / Rrim(I) all: 0.068 / Net I/σ(I): 19.78
Reflection shellResolution: 2.32→2.42 Å / Num. unique obs: 7364 / CC1/2: 0.978 / Rrim(I) all: 0.544

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→68.236 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 3142 5 %
Rwork0.1901 --
obs0.1927 62889 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.32→68.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 0 8 182 10194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810200
X-RAY DIFFRACTIONf_angle_d0.89413764
X-RAY DIFFRACTIONf_dihedral_angle_d10.1646164
X-RAY DIFFRACTIONf_chiral_restr0.0561556
X-RAY DIFFRACTIONf_plane_restr0.0061776
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.35630.33041380.27552611X-RAY DIFFRACTION97
2.3563-2.39490.34751410.25232690X-RAY DIFFRACTION100
2.3949-2.43620.28971430.23682715X-RAY DIFFRACTION100
2.4362-2.48050.31481420.23112702X-RAY DIFFRACTION100
2.4805-2.52820.27031420.21832704X-RAY DIFFRACTION100
2.5282-2.57980.29891430.2182723X-RAY DIFFRACTION100
2.5798-2.63590.27161420.21622694X-RAY DIFFRACTION100
2.6359-2.69720.28891420.2282705X-RAY DIFFRACTION100
2.6972-2.76470.3121430.22392704X-RAY DIFFRACTION100
2.7647-2.83940.3051430.21572716X-RAY DIFFRACTION100
2.8394-2.9230.31751440.21432743X-RAY DIFFRACTION100
2.923-3.01730.26361420.21582703X-RAY DIFFRACTION100
3.0173-3.12520.28071450.21342745X-RAY DIFFRACTION100
3.1252-3.25030.28591430.21362716X-RAY DIFFRACTION100
3.2503-3.39820.24311420.21422707X-RAY DIFFRACTION100
3.3982-3.57740.23881430.21042721X-RAY DIFFRACTION99
3.5774-3.80150.33091270.25662470X-RAY DIFFRACTION90
3.8015-4.0950.23371410.18792669X-RAY DIFFRACTION97
4.095-4.5070.18191460.13912769X-RAY DIFFRACTION100
4.507-5.1590.18151470.13572790X-RAY DIFFRACTION100
5.159-6.4990.19041480.16332817X-RAY DIFFRACTION100
6.499-68.2360.18191550.14522933X-RAY DIFFRACTION99

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