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

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Basic information

Entry
Database: PDB / ID: 4wku
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 / n-Alkylboronic acid inhibitors of PvdQ / 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
hexyl(trihydroxy)borate(1-) / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWu, R. / Clevenger, K.D. / 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 1.1Dec 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_prerelease_seq / pdbx_struct_oper_list / refine_hist / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_keywords.text
Revision 1.2Nov 6, 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
B: Acyl-homoserine lactone acylase PvdQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,24619
Polymers78,6252
Non-polymers1,62117
Water9,872548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11590 Å2
ΔGint-62 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.131, 168.243, 94.945
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: 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
#2: 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
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-3QJ / hexyl(trihydroxy)borate(1-)


Mass: 147.000 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H16BO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / 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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / 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 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2→39.262 Å / Num. obs: 65037 / % possible obs: 99.2 % / Redundancy: 5.1 % / Net I/σ(I): 5.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2→39.262 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 3315 5.1 %
Rwork0.1798 --
obs0.1816 65037 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→39.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5538 0 105 548 6191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035790
X-RAY DIFFRACTIONf_angle_d0.757848
X-RAY DIFFRACTIONf_dihedral_angle_d14.6512161
X-RAY DIFFRACTIONf_chiral_restr0.052830
X-RAY DIFFRACTIONf_plane_restr0.0031039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02860.40521370.34582502X-RAY DIFFRACTION98
2.0286-2.05880.34831440.29972499X-RAY DIFFRACTION98
2.0588-2.0910.29431200.27762556X-RAY DIFFRACTION99
2.091-2.12530.29731450.26042532X-RAY DIFFRACTION99
2.1253-2.16190.27631420.23882542X-RAY DIFFRACTION99
2.1619-2.20130.2471400.22812544X-RAY DIFFRACTION99
2.2013-2.24360.29171230.22222545X-RAY DIFFRACTION99
2.2436-2.28940.26561420.21052527X-RAY DIFFRACTION99
2.2894-2.33920.26131280.20912588X-RAY DIFFRACTION99
2.3392-2.39360.2341450.19622526X-RAY DIFFRACTION99
2.3936-2.45340.19581200.19742607X-RAY DIFFRACTION99
2.4534-2.51970.23731500.19462569X-RAY DIFFRACTION100
2.5197-2.59390.2341320.19172576X-RAY DIFFRACTION100
2.5939-2.67760.23481200.18482584X-RAY DIFFRACTION100
2.6776-2.77320.21621370.18312588X-RAY DIFFRACTION100
2.7732-2.88420.21561230.17072629X-RAY DIFFRACTION100
2.8842-3.01550.22381410.17072553X-RAY DIFFRACTION100
3.0155-3.17440.20661360.16952617X-RAY DIFFRACTION100
3.1744-3.37320.18641520.16262582X-RAY DIFFRACTION100
3.3732-3.63340.18631320.15772609X-RAY DIFFRACTION100
3.6334-3.99880.1921510.14272603X-RAY DIFFRACTION99
3.9988-4.57660.16361660.13352566X-RAY DIFFRACTION99
4.5766-5.76320.17461490.14342617X-RAY DIFFRACTION98
5.7632-39.26970.1871400.16112661X-RAY DIFFRACTION96
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)
13.9799-2.2939-2.17082.3630.38464.0925-0.1095-0.22430.15320.27970.1496-0.19580.11410.3364-0.07610.1139-0.0027-0.04170.2568-0.01650.15543.131133.555923.152
21.7615-1.02681.3671.6276-1.42462.6142-0.01230.13670.1324-0.0693-0.0511-0.129-0.10.20890.07120.1473-0.03630.00720.1699-0.02590.197234.328946.28043.8325
31.14650.14640.01684.4632-3.693.068-0.1098-0.23180.26420.38870.32330.3485-0.7493-0.5296-0.17290.23410.05410.00240.2091-0.04850.259321.928451.393215.4739
43.2360.2384-1.14091.6060.10042.3598-0.0163-0.23660.39860.1030.1697-0.1515-0.04930.212-0.1680.13690.0143-0.03970.178-0.03630.198541.986545.144915.7816
51.2218-0.55760.31640.4542-0.411.30890.01010.03950.06860.07490.06470.0867-0.00330.0271-0.07560.1539-0.00230.00550.1567-0.0040.190327.756746.26774.4116
62.3058-0.72-1.73437.97491.40162.1031-0.1230.89680.272-0.7956-0.08730.5595-0.7867-0.69040.25330.4010.0719-0.06580.42570.05670.33338.54156.186-17.4167
70.7911-0.31580.29540.57080.02520.72780.0154-0.091-0.06730.02080.00970.09520.1109-0.1368-0.04030.1151-0.03670.01770.15690.01470.162315.895832.98617.0227
81.10960.44110.75851.53630.47471.86020.0420.1424-0.0809-0.28720.05510.09290.32380.2501-0.08640.29420.0658-0.02630.1412-0.00060.188532.613817.4406-6.2003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 120 )
4X-RAY DIFFRACTION4chain 'A' and (resid 121 through 150 )
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 184 )
6X-RAY DIFFRACTION6chain 'A' and (resid 185 through 192 )
7X-RAY DIFFRACTION7chain 'B' and (resid 218 through 528 )
8X-RAY DIFFRACTION8chain 'B' and (resid 529 through 764 )

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