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

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Basic information

Entry
Database: PDB / ID: 2wyc
TitleThe quorum quenching N-acyl homoserine lactone acylase PvdQ in complex with 3-oxo-lauric acid
Components(ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ...) x 2
KeywordsHYDROLASE / ZYMOGEN / PERIPLASM
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / 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 amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / 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 (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / 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
3-OXODODECANOIC ACID / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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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)80,20413
Polymers79,0832
Non-polymers1,12111
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10220 Å2
ΔGint-52.02 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.800, 166.500, 94.300
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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ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ... , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 407 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-3LA / 3-OXODODECANOIC ACID / 3-OXO-LAURIC ACID


Mass: 214.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H22O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.95 Å3/Da / Density % sol: 58.3 % / Description: NONE
Crystal growpH: 9 / Details: 24% PEG 6000, 100 MM BICINE PH 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→48.9 Å / Num. obs: 75009 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.69 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.53
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.72 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.16 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0096refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.105 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.18985 3759 5 %RANDOM
Rwork0.16294 ---
obs0.16426 70962 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.404 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.42 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5526 0 73 396 5995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1211.9647930
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03423.275284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.28815911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.921560
X-RAY DIFFRACTIONr_chiral_restr0.0790.2837
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_it0.4621.53610
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87525781
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.62732222
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8034.52149
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 272 -
Rwork0.201 5186 -
obs--99.89 %
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)
11.32980.9718-1.47772.1259-1.12713.1296-0.01240.30710.0162-0.43870.1158-0.1698-0.2217-0.1056-0.10350.32080.03820.04560.1304-0.0060.129632.68468.41131.368
22.5481-0.0992-0.61490.4813-0.01170.9981-0.03640.0272-0.1322-0.0310.0101-0.06820.07510.09370.02640.01450.0076-0.0020.02220.00770.046744.79235.0747.063
31.05890.0828-0.11710.90750.06451.07410.0064-0.08610.11650.03860.0258-0.0292-0.2309-0.033-0.03220.05330.01180.00270.0185-0.010.014729.98656.71960.788
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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