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- PDB-3l91: Structure of Pseudomonas aerugionsa PvdQ bound to octanoate -

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Basic information

Entry
Database: PDB / ID: 3l91
TitleStructure of Pseudomonas aerugionsa PvdQ bound to octanoate
Components
  • Acyl-homoserine lactone acylase pvdQ subunit alpha
  • Acyl-homoserine lactone acylase pvdQ subunit beta
KeywordsHYDROLASE / PvdQ / pyoverdine / acylase / NTN Hydrolase / Quorum sensing / Zymogen
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / pyoverdine biosynthetic process / short-chain fatty acyl-CoA dehydrogenase activity / 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 ...acyl-homoserine-lactone acylase / pyoverdine biosynthetic process / short-chain fatty acyl-CoA dehydrogenase activity / 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/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / 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
OCTANOIC ACID (CAPRYLIC ACID) / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.66 Å
AuthorsDrake, E.J. / Gulick, A.M.
CitationJournal: Acs Chem.Biol. / Year: 2011
Title: Structural characterization and high-throughput screening of inhibitors of PvdQ, an NTN hydrolase involved in pyoverdine synthesis.
Authors: Drake, E.J. / Gulick, A.M.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 17, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)80,40622
Polymers79,0832
Non-polymers1,32420
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12000 Å2
ΔGint17 kcal/mol
Surface area27350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.289, 165.281, 93.998
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: PA01 / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli)
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: PA01 / Gene: PA2385, pvdQ, qsc112 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 58.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 10-15 % PEG4000, 50-100 mM RbCl, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 24, 2009
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 103682 / Num. obs: 103682 / % possible obs: 93.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 19
Reflection shellResolution: 1.65→1.75 Å / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.1 / % possible all: 68.1

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Processing

Software
NameVersionClassification
CHESSA1data collection
SOLVEphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3L94

3l94


Resolution: 1.66→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.343 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS used in final stages
RfactorNum. reflection% reflectionSelection details
Rfree0.18536 5242 5.1 %RANDOM
Rwork0.1675 ---
all0.16842 103682 --
obs0.16842 98384 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.171 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0 Å20 Å2
2--1.44 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.66→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5449 0 86 379 5914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225728
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9597778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45823.37270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42415861
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5771553
X-RAY DIFFRACTIONr_chiral_restr0.0920.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214485
X-RAY DIFFRACTIONr_mcbond_it0.6361.53576
X-RAY DIFFRACTIONr_mcangle_it1.21925704
X-RAY DIFFRACTIONr_scbond_it2.12532152
X-RAY DIFFRACTIONr_scangle_it3.6174.52064
LS refinement shellResolution: 1.657→1.699 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 225 -
Rwork0.28 4418 -
obs--57.31 %
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)
10.7105-0.2079-0.30740.2810.13110.9108-0.028-0.0016-0.09310.01970.02270.02280.0619-0.03460.00530.0401-0.01680.00520.08910.01180.071627.06538.15156.126
20.7338-0.0038-0.09070.1457-0.01540.95860.0357-0.0990.0880.04840.0479-0.0038-0.1838-0.0078-0.08360.0925-0.01450.01480.0709-0.01710.073530.20558.46961.329
30.8219-0.2989-0.36360.3036-0.02270.51460.0047-0.0494-0.00750.020.0007-0.0508-0.01160.14-0.00540.0108-0.0184-0.00790.1043-0.00810.046148.81442.70552.236
40.2233-0.0238-0.30280.9514-0.50821.60770.1230.03280.1847-0.1350.0028-0.1237-0.34580.0754-0.12570.2022-0.04050.08650.05560.02570.17939.87971.39743.163
51.95370.9602-0.30651.6852-1.02853.74540.05770.2105-0.2012-0.34150.0685-0.224-0.02570.2195-0.12620.25640.01170.10080.0495-0.01160.123240.62869.86929.713
61.22050.2201-0.50990.7948-0.14370.9055-0.00720.16670.1215-0.07660.07870.0512-0.1783-0.255-0.07150.07920.0197-0.00030.10090.02070.072120.27659.87949.473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 192
2X-RAY DIFFRACTION2B217 - 279
3X-RAY DIFFRACTION3B280 - 476
4X-RAY DIFFRACTION4B477 - 575
5X-RAY DIFFRACTION5B576 - 636
6X-RAY DIFFRACTION6B637 - 762

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