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- PDB-8sfd: Crystal structure of the engineered SsoPox variant IVB10 -

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Basic information

Entry
Database: PDB / ID: 8sfd
TitleCrystal structure of the engineered SsoPox variant IVB10
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / Lactonase / quorum sensing / phosphotriesterase / arylesterase
Function / homology
Function and homology information


aryldialkylphosphatase / aryldialkylphosphatase activity / 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: To Be Published
Title: Changes in Active Site Loops Conformation Relates to a Transition from Lactonase to Phosphotriesterase
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

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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)35,8175
Polymers35,5151
Non-polymers3024
Water5,693316
1
D: Aryldialkylphosphatase
hetero molecules

D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,63310
Polymers71,0302
Non-polymers6048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5030 Å2
ΔGint-98 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.260, 74.690, 138.710
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 , 5 types, 320 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.31 %
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: 1.03321 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.5→49.19 Å / Num. obs: 54520 / % possible obs: 100 % / Redundancy: 8.25 % / CC1/2: 0.999 / Rrim(I) all: 0.055 / Net I/σ(I): 21.5
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 8.41 % / Num. unique obs: 9490 / CC1/2: 0.945 / Rrim(I) all: 0.599

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.19 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.91 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17272 2726 5 %RANDOM
Rwork0.13848 ---
obs0.14022 51793 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.579 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å2-0 Å2-0 Å2
2---1.31 Å20 Å2
3----1.17 Å2
Refinement stepCycle: 1 / Resolution: 1.5→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2501 0 13 316 2830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122729
X-RAY DIFFRACTIONr_bond_other_d0.0080.0162571
X-RAY DIFFRACTIONr_angle_refined_deg0.8461.6493702
X-RAY DIFFRACTIONr_angle_other_deg0.3551.5736026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5695350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.241518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.25210509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0440.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023136
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02528
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_it2.2472.1621331
X-RAY DIFFRACTIONr_mcbond_other2.2312.1611331
X-RAY DIFFRACTIONr_mcangle_it2.5653.2361683
X-RAY DIFFRACTIONr_mcangle_other2.5643.2371684
X-RAY DIFFRACTIONr_scbond_it3.4352.6351398
X-RAY DIFFRACTIONr_scbond_other3.4342.6361399
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.833.7812013
X-RAY DIFFRACTIONr_long_range_B_refined4.14937.3763277
X-RAY DIFFRACTIONr_long_range_B_other4.08835.7763263
X-RAY DIFFRACTIONr_rigid_bond_restr5.44835300
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 197 -
Rwork0.213 3756 -
obs--99.97 %

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