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

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Basic information

Entry
Database: PDB / ID: 4wkt
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
1-BUTANE BORONIC ACID / Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.782 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
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
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
Revision 1.2Nov 13, 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)80,38521
Polymers78,6252
Non-polymers1,76019
Water11,710650
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-56 kcal/mol
Surface area28600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.294, 167.512, 95.025
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-BUB / 1-BUTANE BORONIC ACID


Mass: 101.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11BO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 59.9 %
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: 1.78→47.513 Å / Num. obs: 92191 / % possible obs: 99.9 % / Redundancy: 5.7 % / Net I/σ(I): 10.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1678) / Classification: refinement
RefinementResolution: 1.782→47.513 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1918 2000 2.17 %
Rwork0.1654 --
obs0.166 92148 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.782→47.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5522 0 114 650 6286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075836
X-RAY DIFFRACTIONf_angle_d1.0437911
X-RAY DIFFRACTIONf_dihedral_angle_d15.4812188
X-RAY DIFFRACTIONf_chiral_restr0.043833
X-RAY DIFFRACTIONf_plane_restr0.0051047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.782-1.82610.31271390.29526265X-RAY DIFFRACTION99
1.8261-1.87540.30971420.26416406X-RAY DIFFRACTION100
1.8754-1.93060.26431420.23946377X-RAY DIFFRACTION100
1.9306-1.99290.21281420.21266406X-RAY DIFFRACTION100
1.9929-2.06420.2471420.20086423X-RAY DIFFRACTION100
2.0642-2.14680.21081420.18086370X-RAY DIFFRACTION100
2.1468-2.24450.21981420.17026426X-RAY DIFFRACTION100
2.2445-2.36280.18231420.16256407X-RAY DIFFRACTION100
2.3628-2.51090.22331440.16386455X-RAY DIFFRACTION100
2.5109-2.70470.18941420.16176468X-RAY DIFFRACTION100
2.7047-2.97690.17441440.15996446X-RAY DIFFRACTION100
2.9769-3.40750.19061440.15686496X-RAY DIFFRACTION100
3.4075-4.29270.15421440.14046520X-RAY DIFFRACTION100
4.2927-47.52940.16971490.14586683X-RAY DIFFRACTION99
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)
10.6943-0.12970.19130.22160.15720.4798-0.0214-0.1166-0.01480.05470.03340.05510.1014-0.112-0.02370.2059-0.02610.00970.17690.01940.201821.392432.51258.797
21.2332-0.22180.48080.69650.12821.2185-0.0962-0.00230.2941-0.0963-0.0079-0.0622-0.142-0.11250.07050.18340.00980.01360.20910.00880.255317.908349.22730.3327
30.941-0.76150.31160.864-0.07470.71680.0174-0.218-0.28180.01660.08250.23840.2006-0.3078-0.08270.2499-0.080.01690.30550.06010.30410.803825.26358.7836
41.26140.49890.99241.46320.59642.02060.00410.2053-0.1298-0.25220.12210.1080.31360.2282-0.10640.33860.0308-0.01190.2208-0.00120.262932.305217.3843-5.9161
52.62762.9521-1.79184.1644-0.65913.38330.0257-1.54661.26141.71050.0280.3961-0.9892-0.2906-0.26120.55020.1023-0.07280.4426-0.21730.402641.171744.896230.6481
63.7776-2.6593-2.54373.52492.53834.0649-0.183-0.32580.03090.30120.2562-0.12860.30920.3247-0.08180.19860.0513-0.02250.2265-0.02170.169143.279830.94721.6926
71.9224-0.88521.23511.1998-1.25462.5998-0.02540.10280.1982-0.0285-0.0273-0.1208-0.09540.13480.05510.1633-0.0283-0.0070.1529-0.01690.195434.706545.8054.2528
81.6658-0.69660.80495.6662-4.37863.4765-0.2447-0.27450.15290.66120.17250.2133-1.0863-0.51370.01630.28450.0545-0.00890.2518-0.05760.281522.041751.281415.5111
93.79850.1041-1.33871.37230.03282.7345-0.0822-0.29780.48230.12480.1696-0.184-0.14270.2468-0.06590.20480.0171-0.0550.1971-0.03990.220641.962544.875315.7007
105.0462.0118-4.74421.0233-1.98364.79340.09070.10920.6803-0.02370.19460.0902-0.54740.3292-0.36510.2529-0.0528-0.03860.2437-0.01680.278241.910451.02636.2695
113.0438-0.08623.08150.7317-0.26363.51080.01470.09150.01130.04730.0357-0.00140.05770.0962-0.05980.17420.02560.02540.21650.00760.193923.256544.60553.3889
125.2638-1.17131.79177.7901-1.59591.5075-0.19431.03650.2191-0.6419-0.06780.4403-0.8156-0.40310.29970.42260.1312-0.03810.48750.07840.27739.04556.3409-16.9695
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 218 through 316 )
2X-RAY DIFFRACTION2chain 'C' and (resid 317 through 383 )
3X-RAY DIFFRACTION3chain 'C' and (resid 384 through 528 )
4X-RAY DIFFRACTION4chain 'C' and (resid 529 through 764 )
5X-RAY DIFFRACTION5chain 'A' and (resid 28 through 33 )
6X-RAY DIFFRACTION6chain 'A' and (resid 34 through 49 )
7X-RAY DIFFRACTION7chain 'A' and (resid 50 through 106 )
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 120 )
9X-RAY DIFFRACTION9chain 'A' and (resid 121 through 150 )
10X-RAY DIFFRACTION10chain 'A' and (resid 151 through 158 )
11X-RAY DIFFRACTION11chain 'A' and (resid 159 through 184 )
12X-RAY DIFFRACTION12chain 'A' and (resid 185 through 192 )

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