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- PDB-5vrk: Crystal structure of SsoPox AsA6 mutant (F46L-C258A-W263M-I280T) ... -

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Basic information

Entry
Database: PDB / ID: 5vrk
TitleCrystal structure of SsoPox AsA6 mutant (F46L-C258A-W263M-I280T) - open form
ComponentsAryldialkylphosphatase
KeywordsHYDROLASE / lactonase / phosphotriesterase / mutants / quorum sensing / organophosphate / organophosphorous / insecticides.
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 hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / : / Aryldialkylphosphatase
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHiblot, J. / Gotthard, G. / Jacquet, P. / Daude, D. / Bergonzi, C. / Chabriere, E. / Elias, M.
CitationJournal: Sci Rep / Year: 2017
Title: Rational engineering of a native hyperthermostable lactonase into a broad spectrum phosphotriesterase.
Authors: Jacquet, P. / Hiblot, J. / Daude, D. / Bergonzi, C. / Gotthard, G. / Armstrong, N. / Chabriere, E. / Elias, M.
History
DepositionMay 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 2.0Aug 18, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_2 / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aryldialkylphosphatase
B: Aryldialkylphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,17217
Polymers71,0502
Non-polymers1,12215
Water11,422634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-63 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.280, 137.200, 49.360
Angle α, β, γ (deg.)90.00, 98.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 35524.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97VT7, aryldialkylphosphatase

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Non-polymers , 5 types, 649 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20-30 % (w/v) PEG 8000 and 50 mM Tris-HCl buffer (pH 8)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.4→48.7 Å / Num. obs: 121915 / % possible obs: 96.1 % / Redundancy: 3.44 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.07
Reflection shellResolution: 1.4→1.5 Å / Rmerge(I) obs: 0.334

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vc5

2vc5


Resolution: 1.4→45.97 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.336 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17539 6096 5 %RANDOM
Rwork0.13902 ---
obs0.14083 115818 96.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.065 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.21 Å2
2---0.17 Å2-0 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 1.4→45.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 62 634 5700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195480
X-RAY DIFFRACTIONr_bond_other_d0.0020.025399
X-RAY DIFFRACTIONr_angle_refined_deg1.2781.9767423
X-RAY DIFFRACTIONr_angle_other_deg1.876312476
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8885694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27624.387253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62151011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2711537
X-RAY DIFFRACTIONr_chiral_restr0.0860.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026223
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021218
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_it3.5261.5652665
X-RAY DIFFRACTIONr_mcbond_other3.5261.5642664
X-RAY DIFFRACTIONr_mcangle_it3.7282.3543378
X-RAY DIFFRACTIONr_mcangle_other3.7282.3543379
X-RAY DIFFRACTIONr_scbond_it4.5212.0352815
X-RAY DIFFRACTIONr_scbond_other4.522.0352815
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4382.884040
X-RAY DIFFRACTIONr_long_range_B_refined5.11515.337151
X-RAY DIFFRACTIONr_long_range_B_other4.6514.3786799
X-RAY DIFFRACTIONr_rigid_bond_restr21.105310879
X-RAY DIFFRACTIONr_sphericity_free32.7735143
X-RAY DIFFRACTIONr_sphericity_bonded10.532511258
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 437 -
Rwork0.222 8309 -
obs--93.66 %
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)
10.1390.0046-0.03010.19290.00870.20020.0155-0.01970.01960.01960.00830.0095-0.02760.0084-0.02380.008-0.00290.00480.0045-0.00180.0059-20.409119.4464-7.599
20.18760.0125-0.02390.18590.01420.1468-0.02190.0102-0.02920.00940.00690.01850.0186-0.01980.01510.0055-0.00150.00450.0057-0.00420.0092-37.5064-10.7019-27.3634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 314
2X-RAY DIFFRACTION1A401 - 407
3X-RAY DIFFRACTION2B1 - 314
4X-RAY DIFFRACTION2B401 - 408

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