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- PDB-3src: Structure of Pseudomonas aeruginosa PvdQ bound to NS2028 -

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Basic information

Entry
Database: PDB / ID: 3src
TitleStructure of Pseudomonas aeruginosa PvdQ bound to NS2028
Components(Acyl-homoserine lactone acylase pvdQ) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / nrps tailoring / acylase / liganded / 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-28N / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGulick, A.M. / Drake, E.J.
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
DepositionJul 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Sep 13, 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 1.3Oct 30, 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)79,77221
Polymers78,3862
Non-polymers1,38619
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint1 kcal/mol
Surface area27220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.565, 165.828, 93.951
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: 17896.076 Da / Num. of mol.: 1 / Fragment: alpha subunit (UNP residues 29-191)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: PA2385, PA2385 PvdQ, qsc112 / Plasmid: pED485 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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: PAO1 / Gene: PA2385, PA2385 PvdQ, qsc112 / Plasmid: pED485 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-28N / 8-bromo-4H-[1,2,4]oxadiazolo[3,4-c][1,4]benzoxazin-1-one


Mass: 269.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H5BrN2O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 3 Å3/Da / Density % sol: 58.94 %
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: BL9-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 24, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2→39 Å / Num. all: 63767 / Num. obs: 61883 / % possible obs: 97.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.8 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.9
Reflection shellResolution: 2→2.1 Å / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 1.7 / % possible all: 82

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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 3L91

3l91


Resolution: 2→39 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.78 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.164 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22179 3108 5 %RANDOM
Rwork0.19667 ---
all0.19796 61882 --
obs0.19796 58774 97.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å2-0 Å2
2--1.43 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5447 0 87 237 5771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0215698
X-RAY DIFFRACTIONr_angle_refined_deg1.2651.9637735
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7885718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51723.42269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74815851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8311553
X-RAY DIFFRACTIONr_chiral_restr0.080.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214473
X-RAY DIFFRACTIONr_mcbond_it0.5241.53565
X-RAY DIFFRACTIONr_mcangle_it0.97925681
X-RAY DIFFRACTIONr_scbond_it1.58432133
X-RAY DIFFRACTIONr_scangle_it2.6814.52053
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 165 -
Rwork0.279 3491 -
obs--78.22 %

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