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- PDB-2wyd: The quorum quenching N-acyl homoserine lactone acylase PvdQ in co... -

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Basic information

Entry
Database: PDB / ID: 2wyd
TitleThe quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with dodecanoic acid
Components
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
KeywordsHYDROLASE / ZYMOGEN / PERIPLASM
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / pyoverdine biosynthetic process / quorum sensing / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic / identical protein binding / cytoplasm
Similarity search - Function
Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsBokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: The Quorum-Quenching N-Acyl Homoserine Lactone Acylase Pvdq is an Ntn-Hydrolase with an Unusual Substrate-Binding Pocket
Authors: Bokhove, M. / Nadal Jimenez, P. / Quax, W.J. / Dijkstra, B.W.
History
DepositionNov 16, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
B: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,22012
Polymers79,0832
Non-polymers1,13710
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10890 Å2
ΔGint-45.09 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.775, 166.366, 94.313
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 ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA / ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA


Mass: 18592.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. DH10B
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#2: Protein ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA / ACYL-HSL ACYLASE PVDQ SUBUNIT BETA


Mass: 60489.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 SUBSTR. DH10B
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE
Crystal growpH: 9 / Details: 24% PEG 6000, 100 MM BICINE PH 9.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→39.13 Å / Num. obs: 73345 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 4.24 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 1.63 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0096refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.901→39.129 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.684 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.12 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 3686 5.08 %RANDOM
Rwork0.1674 ---
obs0.169 73309 98.059 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.768 Å2
Baniso -1Baniso -2Baniso -3
1--0.083 Å20 Å2-0 Å2
2--0.753 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.901→39.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 76 432 6034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225840
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1441.9647937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6523.298285
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50315912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9841560
X-RAY DIFFRACTIONr_chiral_restr0.0760.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214591
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_it0.451.53611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8525781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6332229
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7614.52155
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 237 -
Rwork0.25 4429 -
obs--85.709 %
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)
10.85930.6174-0.89631.5109-0.74132.1199-0.02380.27620.0432-0.33750.0887-0.0933-0.1467-0.0819-0.06480.26470.03010.02670.14410.01120.112232.90968.41431.293
22.0827-0.131-0.48490.428-0.01610.7917-0.03960.0272-0.1159-0.03440.0067-0.04830.06890.07920.03290.0150.00630.0020.01490.00360.031344.8234.8647.177
31.01780.1032-0.13390.87560.01740.93320.0135-0.08650.11610.0470.0159-0.0167-0.1928-0.0222-0.02930.04320.00740.00280.0094-0.01020.014430.1256.70960.799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B323 - 480
2X-RAY DIFFRACTION2A51 - 95
3X-RAY DIFFRACTION2A129 - 168
4X-RAY DIFFRACTION2B75 - 155
5X-RAY DIFFRACTION2B206 - 250
6X-RAY DIFFRACTION3A6 - 50
7X-RAY DIFFRACTION3A96 - 128
8X-RAY DIFFRACTION3B1 - 74
9X-RAY DIFFRACTION3B156 - 205
10X-RAY DIFFRACTION3B251 - 322
11X-RAY DIFFRACTION3B481 - 546

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