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- PDB-4bth: The LeuA146Trp,PheB24Tyr Double Mutant of the Quorum Quenching N-... -

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Basic information

Entry
Database: PDB / ID: 4bth
TitleThe LeuA146Trp,PheB24Tyr Double Mutant of the Quorum Quenching N-acyl Homoserine Lactone Acylase PvdQ Has an Altered Substrate Specificity Towards Small Acyl Chains
Components
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT ALPHA
  • ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
KeywordsHYDROLASE / ZYMOGEN / QUORUM QUENCHING
Function / homology
Function and homology information


acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / bacterial-type flagellum-dependent swarming motility / single-species biofilm formation / antibiotic biosynthetic process / periplasmic space / response to antibiotic ...acyl-homoserine-lactone acylase / short-chain fatty acyl-CoA dehydrogenase activity / pyoverdine biosynthetic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / quorum sensing / 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 amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob ...Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / 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
Acyl-homoserine lactone acylase PvdQ
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKoch, G. / Nadal-Jimenez, P. / Reis, C.R. / Muntendam, R. / Bokhove, M. / Melillo, E. / Dijkstra, B.W. / Cool, R.H. / Quax, W.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Reducing Virulence of the Human Pathogen Burkholderia by Altering the Substrate Specificity of the Quorum-Quenching Acylase Pvdq
Authors: Koch, G. / Nadal-Jimenez, P. / Reis, C.R. / Muntendam, R. / Bokhove, M. / Melillo, E. / Dijkstra, B.W. / Cool, R.H. / Quax, W.J.
History
DepositionJun 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 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 SUBUNIT ALPHA
B: ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6327
Polymers79,1722
Non-polymers4605
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-57.3 kcal/mol
Surface area28130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.353, 167.133, 94.443
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 SUBUNIT ALPHA / AHL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ SUBUNIT ALPHA /


Mass: 18665.969 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DH10B
References: UniProt: Q9I194, acyl-homoserine-lactone acylase
#2: Protein ACYL-HOMOSERINE LACTONE ACYLASE PVDQ SUBUNIT BETA / AHL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ / ACYL-HSL ACYLASE PVDQ SUBUNIT BETA


Mass: 60505.918 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: PMCTNDE / Production host: ESCHERICHIA COLI K-12 (bacteria) / Variant (production host): DH10B
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.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 3.03 Å3/Da / Density % sol: 59.4 % / Description: NONE
Crystal growpH: 9.1
Details: PROTEIN WAS CRYSTALLIZED FROM 24% PEG 6000, 100 MM BICINE PH 9.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9786
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→83.57 Å / Num. obs: 71419 / % possible obs: 94.6 % / Observed criterion σ(I): 1 / Redundancy: 4.82 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.61
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.81 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.21 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0091refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WYE

2wye


Resolution: 1.9→62.584 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.44 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 3591 5.05 %RANDOM
Rwork0.1794 ---
obs0.181 67730 94.198 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 37.128 Å2
Baniso -1Baniso -2Baniso -3
1--0.599 Å20 Å20 Å2
2--1.175 Å20 Å2
3----0.576 Å2
Refinement stepCycle: LAST / Resolution: 1.9→62.584 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 30 254 5821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9587769
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.615712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.27823.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07115896
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3571557
X-RAY DIFFRACTIONr_chiral_restr0.0810.2828
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214487
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22706
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23821
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2195
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0110.15715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.0180.157769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.0330.21945
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.0170.47305
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 231 -
Rwork0.285 4904 -
obs--96.486 %
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)
11.38691.1251-1.91572.5848-1.63713.87030.00050.34160.0509-0.52080.1265-0.2148-0.2018-0.1862-0.12710.35660.03980.05180.17380.0080.144332.740768.750231.199
22.9364-0.1652-0.68950.454-0.1021.1922-0.06560.0593-0.1468-0.06460.0147-0.07220.0710.09450.05090.03440.00650.00750.03050.00140.034145.05535.309147.1397
31.22620.134-0.12280.9139-0.0231.13530.0013-0.10810.15830.06890.0349-0.0233-0.2524-0.0364-0.03630.0620.01660.00180.0335-0.01480.022630.073557.029661.0042
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B323 - 480
2X-RAY DIFFRACTION2A51 - 95
3X-RAY DIFFRACTION2A129 - 168
4X-RAY DIFFRACTION2B75 - 155
5X-RAY DIFFRACTION2B206 - 250
6X-RAY DIFFRACTION3A6 - 50
7X-RAY DIFFRACTION3A96 - 128
8X-RAY DIFFRACTION3B1 - 74
9X-RAY DIFFRACTION3B156 - 205
10X-RAY DIFFRACTION3B251 - 322
11X-RAY DIFFRACTION3B481 - 546

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