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- PDB-4k2f: Structure of Pseudomonas aeruginosa PvdQ bound to BRD-A08522488 -

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Basic information

Entry
Database: PDB / ID: 4k2f
TitleStructure of Pseudomonas aeruginosa PvdQ bound to BRD-A08522488
Components(Acyl-homoserine lactone acylase PvdQ) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / amidohydrolase / bacterial protein / catalytic domain / high-throughput screening assays / molecular sequence data / oligopeptides / small molecule libraries / structure-activity relationship / HYDROLASE-HYDROLASE INHIBITOR complex
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
Chem-A08 / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsDrake, E.J. / Wurst, J.M. / Theriault, J.R. / Munoz, B. / Gulick, A.M.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Identification of Inhibitors of PvdQ, an Enzyme Involved in the Synthesis of the Siderophore Pyoverdine.
Authors: Wurst, J.M. / Drake, E.J. / Theriault, J.R. / Jewett, I.T. / VerPlank, L. / Perez, J.R. / Dandapani, S. / Palmer, M. / Moskowitz, S.M. / Schreiber, S.L. / Munoz, B. / Gulick, A.M.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 20, 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 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-homoserine lactone acylase PvdQ
B: Acyl-homoserine lactone acylase PvdQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,96713
Polymers79,0832
Non-polymers88411
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9560 Å2
ΔGint-28 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.280, 166.020, 94.190
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 / AHL acylase PvdQ / Acyl-HSL acylase PvdQ


Mass: 18592.918 Da / Num. of mol.: 1 / Fragment: alpha subunit (UNP residues 24-193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pvdQ, qsc112, PA2385 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#2: Protein Acyl-homoserine lactone acylase PvdQ / AHL acylase PvdQ / Acyl-HSL acylase PvdQ


Mass: 60489.918 Da / Num. of mol.: 1 / Fragment: beta subunit (UNP residues 217-762)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pvdQ, qsc112, PA2385 / 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.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-A08 / (2S)-(4-chlorophenyl)(6-chloropyridin-2-yl)ethanenitrile


Mass: 263.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H8Cl2N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-15% PEG4000, 50-100 mM rubidium chloride, 50 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 12, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.99→50.7 Å / Num. obs: 60638 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.4
Reflection shellResolution: 1.99→2.1 Å / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.2 / % possible all: 98.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
MOLREPphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3L94

3l94


Resolution: 1.99→50.69 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.953 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20563 3199 5 %RANDOM
Rwork0.16767 ---
obs0.16962 60638 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.822 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å2-0 Å20 Å2
2--0.97 Å2-0 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.99→50.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5461 0 57 520 6038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0225675
X-RAY DIFFRACTIONr_angle_refined_deg2.0471.9597718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.423.358268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2115856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6041553
X-RAY DIFFRACTIONr_chiral_restr0.1710.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214458
X-RAY DIFFRACTIONr_mcbond_it1.31.53554
X-RAY DIFFRACTIONr_mcangle_it2.10125667
X-RAY DIFFRACTIONr_scbond_it3.50432121
X-RAY DIFFRACTIONr_scangle_it5.4184.52047
LS refinement shellResolution: 1.99→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 215 -
Rwork0.196 4429 -
obs--98.1 %

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