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- PDB-8sf9: Crystal structure of the engineered SsoPox variant IG7 - Alternat... -

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Basic information

Entry
Database: PDB / ID: 8sf9
TitleCrystal structure of the engineered SsoPox variant IG7 - Alternative 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: 1.8 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
Agence Nationale de la Recherche (ANR)10-IAHU-03 France
Other governmentMndrive
Other governmentBiotechnology Institute
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

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Assembly

Deposited unit
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6913
Polymers35,5761
Non-polymers1152
Water2,774154
1
D: Aryldialkylphosphatase
hetero molecules

D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3816
Polymers71,1522
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3490 Å2
ΔGint-71 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.520, 74.960, 137.300
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: 35575.762 Da / Num. of mol.: 1 / Mutation: V27G, R154K, I280T
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: IG7
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.33 Å3/Da / Density % sol: 47.17 %
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: 0.968 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.8→46.11 Å / Num. obs: 202464 / % possible obs: 98.8 % / Redundancy: 3.43 % / CC1/2: 0.998 / Rrim(I) all: 0.058 / Net I/σ(I): 11.34
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 8881 / CC1/2: 0.832 / Rrim(I) all: 0.77

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→46.07 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.006 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23372 1562 5 %RANDOM
Rwork0.20044 ---
obs0.20218 29661 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.172 Å2
Baniso -1Baniso -2Baniso -3
1-4.54 Å2-0 Å2-0 Å2
2---2.26 Å20 Å2
3----2.28 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2258 0 0 154 2412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122465
X-RAY DIFFRACTIONr_bond_other_d0.0120.0162327
X-RAY DIFFRACTIONr_angle_refined_deg0.6481.6483347
X-RAY DIFFRACTIONr_angle_other_deg0.4471.5795455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4955320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.626513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.47610463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0310.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02464
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3264.4871217
X-RAY DIFFRACTIONr_mcbond_other4.3244.4861217
X-RAY DIFFRACTIONr_mcangle_it6.2636.6871537
X-RAY DIFFRACTIONr_mcangle_other6.2656.6881538
X-RAY DIFFRACTIONr_scbond_it5.4575.1961248
X-RAY DIFFRACTIONr_scbond_other5.4555.1971249
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.3687.5531804
X-RAY DIFFRACTIONr_long_range_B_refined11.71161.7082880
X-RAY DIFFRACTIONr_long_range_B_other11.7458.8892845
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 114 -
Rwork0.375 2160 -
obs--99.96 %

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