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- PDB-4rdy: Crystal structure of VmoLac bound to 3-oxo-C10 AHL -

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Basic information

Entry
Database: PDB / ID: 4rdy
TitleCrystal structure of VmoLac bound to 3-oxo-C10 AHL
ComponentsParathion hydrolase
KeywordsHYDROLASE / lactonase / quorum sensing / aryldialkylphosphatase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / 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
Chem-3M5 / : / Parathion hydrolase
Similarity search - Component
Biological speciesVulcanisaeta moutnovskia (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHiblot, J. / Bzdrenga, J. / Champion, C. / Gotthard, G. / Gonzalez, D. / Chabriere, E. / Elias, M.
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of VmoLac, a tentative quorum quenching lactonase from the extremophilic crenarchaeon Vulcanisaeta moutnovskia.
Authors: Hiblot, J. / Bzdrenga, J. / Champion, C. / Chabriere, E. / Elias, M.
History
DepositionSep 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parathion hydrolase
B: Parathion hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,37223
Polymers71,2082
Non-polymers2,16421
Water11,872659
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9250 Å2
ΔGint-124 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.740, 174.740, 61.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Parathion hydrolase


Mass: 35603.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vulcanisaeta moutnovskia (archaea) / Strain: 768-28 / Gene: VMUT_2255 / Production host: Escherichia coli (E. coli) / References: UniProt: F0QXN6

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Non-polymers , 5 types, 680 molecules

#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-3M5 / 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide / N-(3-Oxodecanoyl)-L-homoserine lactone


Mass: 269.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H23NO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.81 Å3/Da / Density % sol: 67.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VmoLac was concentrated at 20mg/mL, 100 mM Tris, pH 8.5, 1.5 M ammonium sulphate, 12 % v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.95373 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→47.75 Å / Num. obs: 72593 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.75 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.432 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17444 3630 5 %RANDOM
Rwork0.13866 ---
obs0.14047 68963 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.079 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4976 0 130 659 5765
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0195265
X-RAY DIFFRACTIONr_bond_other_d0.0030.025177
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9747129
X-RAY DIFFRACTIONr_angle_other_deg1.0853.00411904
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89723.276232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12715906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3981543
X-RAY DIFFRACTIONr_chiral_restr0.1270.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.025788
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021179
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_it2.0331.9942536
X-RAY DIFFRACTIONr_mcbond_other2.0321.9952537
X-RAY DIFFRACTIONr_mcangle_it2.7052.973169
X-RAY DIFFRACTIONr_mcangle_other2.7052.9713170
X-RAY DIFFRACTIONr_scbond_it3.9832.4432729
X-RAY DIFFRACTIONr_scbond_other3.9832.4432730
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7023.4813949
X-RAY DIFFRACTIONr_long_range_B_refined8.45119.0086768
X-RAY DIFFRACTIONr_long_range_B_other8.4519.0096769
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 267 -
Rwork0.208 5079 -
obs--99.93 %

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