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- PDB-3srb: Structure of Pseudomonas aeruginosa PvdQ bound to SMER28 -

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Basic information

Entry
Database: PDB / ID: 3srb
TitleStructure of Pseudomonas aeruginosa PvdQ bound to SMER28
Components(Acyl-homoserine lactone acylase ...) 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
6-bromo-N-(prop-2-en-1-yl)quinazolin-4-amine / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 1.2Dec 5, 2012Group: Non-polymer description
Revision 1.3Sep 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 1.4Oct 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)79,17613
Polymers78,2572
Non-polymers91911
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-53 kcal/mol
Surface area27390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.961, 166.746, 93.856
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 ... , 2 types, 2 molecules AB

#1: Protein Acyl-homoserine lactone acylase pvdQ / AHL acylase pvdQ / Acyl-HSL acylase pvdQ


Mass: 17766.896 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

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Non-polymers , 4 types, 475 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-28S / 6-bromo-N-(prop-2-en-1-yl)quinazolin-4-amine / SMER28


Mass: 264.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10BrN3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.02 Å3/Da / Density % sol: 59.32 %
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: BL11-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 6, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→35 Å / Num. all: 95503 / Num. obs: 94858 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.249 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.187 / Mean I/σ(I) obs: 4 / % possible all: 100

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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: 1.8→35 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.975 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.11 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20338 4386 5 %RANDOM
Rwork0.18808 ---
all0.18887 87481 --
obs0.18887 83095 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.552 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0 Å2
2--0.82 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.8→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5442 0 56 464 5962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225658
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9617701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.8323.396268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14915851
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3561553
X-RAY DIFFRACTIONr_chiral_restr0.0730.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214448
X-RAY DIFFRACTIONr_mcbond_it0.4691.53552
X-RAY DIFFRACTIONr_mcangle_it0.89225661
X-RAY DIFFRACTIONr_scbond_it1.34832106
X-RAY DIFFRACTIONr_scangle_it2.3444.52035
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 307 -
Rwork0.225 6089 -
obs--100 %

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