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- PDB-6z5k: PqsR (MvfR) in complex with antagonist 18 -

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Basic information

Entry
Database: PDB / ID: 6z5k
TitlePqsR (MvfR) in complex with antagonist 18
ComponentsTranscriptional regulator MvfR
KeywordsDNA BINDING PROTEIN / Pseudomonas aeruginosa / Antagonist / Quorum sensing
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-QAE / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.201 Å
AuthorsRichardson, W.K. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Eur.J.Med.Chem. / Year: 2020
Title: Novel quinazolinone inhibitors of the Pseudomonas aeruginosa quorum sensing transcriptional regulator PqsR.
Authors: Grossman, S. / Soukarieh, F. / Richardson, W. / Liu, R. / Mashabi, A. / Emsley, J. / Williams, P. / Camara, M. / Stocks, M.J.
History
DepositionMay 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 7, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0972
Polymers26,7491
Non-polymers3481
Water362
1
AAA: Transcriptional regulator MvfR
hetero molecules

AAA: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1944
Polymers53,4982
Non-polymers6962
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)118.911, 118.911, 115.464
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcriptional regulator MvfR


Mass: 26749.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain UCBPP-PA14) (bacteria)
Strain: UCBPP-PA14 / Gene: mvfR, PA14_51340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z7A6
#2: Chemical ChemComp-QAE / 6-chloranyl-3-[(2-pentyl-2,3-dihydro-1,3-thiazol-4-yl)methyl]quinazolin-4-one


Mass: 347.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H18ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.38 Å3/Da / Density % sol: 71.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM Sodium citrate, 200 mM Ammonium acetate and 5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.2→115.46 Å / Num. obs: 7628 / % possible obs: 92.4 % / Redundancy: 9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.6
Reflection shellResolution: 3.2→3.42 Å / Rmerge(I) obs: 0.398 / Num. unique obs: 1370 / CC1/2: 0.972

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JVC, 6Q7W

4jvc

6q7w


Resolution: 3.201→76.972 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 21.83 / SU ML: 0.345 / Cross valid method: FREE R-VALUE / ESU R: 1.045 / ESU R Free: 0.418
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2613 401 5.282 %
Rwork0.2035 7191 -
all0.206 --
obs-7592 90.467 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 134.248 Å2
Baniso -1Baniso -2Baniso -3
1-4.477 Å22.238 Å20 Å2
2--4.477 Å20 Å2
3----14.523 Å2
Refinement stepCycle: LAST / Resolution: 3.201→76.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 23 2 1623
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0131653
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171535
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.6362244
X-RAY DIFFRACTIONr_angle_other_deg1.0671.5683547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6515202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78121.30492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68515275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0281514
X-RAY DIFFRACTIONr_chiral_restr0.0380.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02358
X-RAY DIFFRACTIONr_nbd_refined0.1920.2318
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21457
X-RAY DIFFRACTIONr_nbtor_refined0.1540.2795
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2783
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.25
X-RAY DIFFRACTIONr_nbd_other0.1530.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.080.24
X-RAY DIFFRACTIONr_mcbond_it5.83514.323811
X-RAY DIFFRACTIONr_mcbond_other5.82614.309809
X-RAY DIFFRACTIONr_mcangle_it9.16821.4811012
X-RAY DIFFRACTIONr_mcangle_other9.1621.4831012
X-RAY DIFFRACTIONr_scbond_it5.31314.792842
X-RAY DIFFRACTIONr_scbond_other5.31114.79843
X-RAY DIFFRACTIONr_scangle_it8.71921.9741232
X-RAY DIFFRACTIONr_scangle_other8.71521.9731233
X-RAY DIFFRACTIONr_lrange_it13.053166.4441770
X-RAY DIFFRACTIONr_lrange_other13.05166.4051771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.201-3.2840.232310.39525X-RAY DIFFRACTION93.4454
3.284-3.3740.399260.324524X-RAY DIFFRACTION93.0626
3.374-3.4720.327280.317492X-RAY DIFFRACTION91.7108
3.472-3.5780.322330.28485X-RAY DIFFRACTION93.6709
3.578-3.6960.264280.237473X-RAY DIFFRACTION92.4354
3.696-3.8250.267290.229460X-RAY DIFFRACTION92.4386
3.825-3.9690.276340.227423X-RAY DIFFRACTION90.495
3.969-4.1310.252180.204438X-RAY DIFFRACTION92.6829
4.131-4.3150.367220.177398X-RAY DIFFRACTION90.3226
4.315-4.5250.234160.164398X-RAY DIFFRACTION91.796
4.525-4.7690.165150.136376X-RAY DIFFRACTION90.0922
4.769-5.0580.18140.148359X-RAY DIFFRACTION89.8795
5.058-5.4070.24120.174339X-RAY DIFFRACTION89.0863
5.407-5.8390.269190.212297X-RAY DIFFRACTION88.764
5.839-6.3940.374140.246286X-RAY DIFFRACTION88.2353
6.394-7.1470.322250.22250X-RAY DIFFRACTION87.5796
7.147-8.2470.211120.195229X-RAY DIFFRACTION86.3799
8.247-10.0870.138120.145192X-RAY DIFFRACTION85
10.087-14.2120.3270.148154X-RAY DIFFRACTION81.3131
14.212-76.970.32160.36993X-RAY DIFFRACTION75

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