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- PDB-4wks: n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Spec... -

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Basic information

Entry
Database: PDB / ID: 4wks
Titlen-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the Quorum-Quenching and Siderophore Biosynthetic Enzyme PvdQ
Components(Acyl-homoserine lactone acylase PvdQ) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PVDQ / n-Alkylboronic Acid / 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
ethylboronic acid / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.629 Å
AuthorsWu, R. / Clevenger, D.K. / Fast, W. / Liu, D.
CitationJournal: Biochemistry / Year: 2014
Title: n-Alkylboronic Acid Inhibitors Reveal Determinants of Ligand Specificity in the Quorum-Quenching and Siderophore Biosynthetic Enzyme PvdQ.
Authors: Clevenger, K.D. / Wu, R. / Liu, D. / Fast, W.
History
DepositionOct 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Nov 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
C: Acyl-homoserine lactone acylase PvdQ
A: Acyl-homoserine lactone acylase PvdQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6993
Polymers78,6252
Non-polymers741
Water14,070781
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7790 Å2
ΔGint-51 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.862, 167.471, 94.450
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 / Acyl-HSL acylase PvdQ


Mass: 60632.078 Da / Num. of mol.: 1 / Fragment: 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
#2: Protein Acyl-homoserine lactone acylase PvdQ / Acyl-HSL acylase PvdQ


Mass: 17993.191 Da / Num. of mol.: 1 / Fragment: UNP residues 28-192
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-3QD / ethylboronic acid


Mass: 73.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7BO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 781 / 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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: Hepes (50 mM) at pH 7.5; RbCl (80 mM); PEG-4000 10% (w/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→42.6 Å / Num. obs: 119528 / % possible obs: 99.5 % / Redundancy: 3.8 % / Net I/σ(I): 12.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M1J

4m1j


Resolution: 1.629→42.587 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 5988 5.01 %
Rwork0.1575 --
obs0.1591 119501 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.629→42.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5516 0 4 781 6301
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195738
X-RAY DIFFRACTIONf_angle_d1.7077819
X-RAY DIFFRACTIONf_dihedral_angle_d14.3382146
X-RAY DIFFRACTIONf_chiral_restr0.108836
X-RAY DIFFRACTIONf_plane_restr0.011049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.629-1.64790.31351920.28183770X-RAY DIFFRACTION99
1.6479-1.66730.28412220.26923722X-RAY DIFFRACTION100
1.6673-1.68760.29921840.25953780X-RAY DIFFRACTION100
1.6876-1.7090.25962010.24283783X-RAY DIFFRACTION100
1.709-1.73150.2442070.2263765X-RAY DIFFRACTION100
1.7315-1.75520.2721930.22893789X-RAY DIFFRACTION100
1.7552-1.78030.26021850.22413792X-RAY DIFFRACTION100
1.7803-1.80690.23911880.20923738X-RAY DIFFRACTION100
1.8069-1.83510.23972080.20113761X-RAY DIFFRACTION100
1.8351-1.86520.22551810.19523810X-RAY DIFFRACTION100
1.8652-1.89730.24872150.183785X-RAY DIFFRACTION100
1.8973-1.93180.19431930.17643766X-RAY DIFFRACTION100
1.9318-1.9690.22492350.16213760X-RAY DIFFRACTION100
1.969-2.00920.16831880.16143802X-RAY DIFFRACTION100
2.0092-2.05290.20042070.15913789X-RAY DIFFRACTION100
2.0529-2.10060.18421740.15773799X-RAY DIFFRACTION100
2.1006-2.15320.19431920.15573801X-RAY DIFFRACTION100
2.1532-2.21140.182260.15223758X-RAY DIFFRACTION100
2.2114-2.27640.17422050.14243766X-RAY DIFFRACTION100
2.2764-2.34990.18751570.14453859X-RAY DIFFRACTION100
2.3499-2.43390.16512050.14633783X-RAY DIFFRACTION100
2.4339-2.53130.18372190.15313805X-RAY DIFFRACTION100
2.5313-2.64650.18172140.15243804X-RAY DIFFRACTION100
2.6465-2.7860.18782060.15263772X-RAY DIFFRACTION99
2.786-2.96050.17932090.1533793X-RAY DIFFRACTION99
2.9605-3.18910.19672090.14933756X-RAY DIFFRACTION99
3.1891-3.50980.17582110.14523801X-RAY DIFFRACTION98
3.5098-4.01740.16781790.1363805X-RAY DIFFRACTION98
4.0174-5.06020.14971970.12643780X-RAY DIFFRACTION97
5.0602-42.60110.18861860.14953819X-RAY DIFFRACTION94
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)
10.8105-0.28710.28320.4630.05860.7025-0.005-0.0815-0.048-0.00630.00310.10120.0998-0.1193-0.0070.1199-0.02220.00670.13230.00640.146316.310332.96266.9336
21.19680.47390.80111.54670.61872.0013-0.03570.1866-0.1059-0.29560.10940.11140.30310.2304-0.07750.29510.0432-0.00430.1629-0.00420.195933.086717.5983-6.0098
33.2502-2.5976-2.28314.12743.74196.6318-0.2027-0.22640.05920.29140.219-0.15750.30010.4386-0.03610.15930.0444-0.02280.22610.00450.14143.671133.05322.5919
41.9937-1.06771.79271.5162-1.74693.7539-0.01010.09340.1059-0.0817-0.0484-0.0863-0.01210.16770.04240.0939-0.03090.00250.0997-0.02150.128534.663446.15714.1609
51.51930.7504-0.41147.9529-5.29823.5387-0.0553-0.19910.08710.52130.14930.3111-0.8164-0.422-0.10560.19550.0419-0.00370.1888-0.05820.22822.187851.344715.5804
63.98980.5-2.57470.9084-0.48223.0302-0.0603-0.13990.24670.05210.1348-0.0818-0.06730.1251-0.08290.1277-0.0118-0.02790.1676-0.04260.162442.258146.619613.5963
73.5938-0.44622.60131.7486-0.47475.4230.03810.0858-0.0192-0.08460.01170.08270.0409-0.0378-0.0910.08490.01350.03310.09050.00080.127620.698746.6597-0.0604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 218 through 528 )
2X-RAY DIFFRACTION2chain 'C' and (resid 529 through 764 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 49 )
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 120 )
6X-RAY DIFFRACTION6chain 'A' and (resid 121 through 158 )
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 192 )

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