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- PDB-4ker: Crystal structure of SsoPox W263V -

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Basic information

Entry
Database: PDB / ID: 4ker
TitleCrystal structure of SsoPox W263V
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / (beta/alpha)8-hydrolase / lactonase
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / : / DI(HYDROXYETHYL)ETHER / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGotthard, G. / Hiblot, J. / Chabriere, E. / Elias, M.
CitationJournal: Plos One / Year: 2013
Title: Differential Active Site Loop Conformations Mediate Promiscuous Activities in the Lactonase SsoPox.
Authors: Hiblot, J. / Gotthard, G. / Elias, M. / Chabriere, E.
History
DepositionApr 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
C: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,20430
Polymers142,2834
Non-polymers1,92126
Water6,575365
1
A: Aryldialkylphosphatase
C: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,09415
Polymers71,1422
Non-polymers95213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-54 kcal/mol
Surface area22760 Å2
MethodPISA
2
B: Aryldialkylphosphatase
D: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,11015
Polymers71,1422
Non-polymers96813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-69 kcal/mol
Surface area23120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.200, 103.500, 151.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 35570.824 Da / Num. of mol.: 4 / Mutation: W263V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: php, php SSO2522, SSO2522 / Plasmid: pET22b-W263V / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-pLysS / References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 6 types, 391 molecules

#2: Chemical
ChemComp-FE2 / FE (II) 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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Tris-HCl, 23-25% PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.99987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.6→45.41 Å / Num. obs: 42787

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→45.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.915 / SU B: 21.536 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23736 2140 5 %RANDOM
Rwork0.16834 ---
obs0.17177 40646 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.623 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å20 Å20 Å2
2---2.73 Å20 Å2
3----3.02 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10024 0 103 365 10492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0210347
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.5671.97313909
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.77951256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.04624.404470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.275151864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9171561
X-RAY DIFFRACTIONr_chiral_restr0.0330.21572
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.0217656
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 148 -
Rwork0.225 2726 -
obs--99.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.54530.25530.08380.61560.02431.75120.044-0.0062-0.00810.068-0.0591-0.0517-0.0439-0.02170.01510.0269-0.004-0.00220.00830.00350.0384-24.1006-13.616826.3201
20.3475-0.0256-0.07480.7307-0.09711.67450.0060.03320.0086-0.0194-0.0092-0.03770.01570.02080.00320.0177-0.0139-0.0250.02160.02970.0496-23.9827-41.185860.112
30.2180.0052-0.22580.72120.01181.98590.0123-0.0010.055-0.0736-0.0103-0.0628-0.11720.0493-0.0020.03330.0040.01490.00460.01050.0504-15.8837-15.5376-11.9504
40.47680.0420.25330.4663-0.10472.04-0.0139-0.00610.03920.04890.01170.0254-0.18110.02450.00220.0557-0.01230.00240.0046-0.00210.018-22.1984-33.508798.5896
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION1A401 - 406
3X-RAY DIFFRACTION2B1 - 314
4X-RAY DIFFRACTION2B401 - 407
5X-RAY DIFFRACTION3C1 - 314
6X-RAY DIFFRACTION3C401 - 407
7X-RAY DIFFRACTION4D1 - 314
8X-RAY DIFFRACTION4D401 - 406

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