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- PDB-6z07: PqsR (MvfR) in complex with antagonist 12 -

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Basic information

Entry
Database: PDB / ID: 6z07
TitlePqsR (MvfR) in complex with antagonist 12
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-Q4E / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 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 7, 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 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
AAA: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1753
Polymers26,7491
Non-polymers4262
Water905
1
AAA: Transcriptional regulator MvfR
hetero molecules

AAA: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3506
Polymers53,4982
Non-polymers8524
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)120.790, 120.790, 114.393
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-Q4E / 3-[(2-~{tert}-butyl-1,3-thiazol-4-yl)methyl]-6-chloranyl-quinazolin-4-one


Mass: 333.836 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16ClN3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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 6% 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: 2.95→60.47 Å / Num. obs: 10879 / % possible obs: 100 % / Redundancy: 9.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.6
Reflection shellResolution: 2.95→3.13 Å / Rmerge(I) obs: 1.079 / Num. unique obs: 1704 / CC1/2: 0.917

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JVC, 6Q7W

4jvc

6q7w


Resolution: 2.95→60.47 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.912 / SU B: 15.511 / SU ML: 0.264 / Cross valid method: FREE R-VALUE / ESU R: 0.392 / ESU R Free: 0.306
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2565 528 4.863 %
Rwork0.1995 --
all0.202 --
obs-10857 99.899 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 120.825 Å2
Baniso -1Baniso -2Baniso -3
1-4.006 Å22.003 Å20 Å2
2--4.006 Å20 Å2
3----12.994 Å2
Refinement stepCycle: LAST / Resolution: 2.95→60.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 28 5 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131657
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171539
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.6352251
X-RAY DIFFRACTIONr_angle_other_deg1.2621.5683553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88321.30492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.72715275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6691514
X-RAY DIFFRACTIONr_chiral_restr0.070.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021853
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
X-RAY DIFFRACTIONr_nbd_refined0.2280.2378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.21575
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2784
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2865
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1690.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4310.216
X-RAY DIFFRACTIONr_nbd_other0.4150.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2320.24
X-RAY DIFFRACTIONr_mcbond_it13.17412.68811
X-RAY DIFFRACTIONr_mcbond_other13.16312.677809
X-RAY DIFFRACTIONr_mcangle_it17.91619.021012
X-RAY DIFFRACTIONr_mcangle_other17.91319.021012
X-RAY DIFFRACTIONr_scbond_it13.41313.454846
X-RAY DIFFRACTIONr_scbond_other13.40713.457847
X-RAY DIFFRACTIONr_scangle_it19.09619.8321239
X-RAY DIFFRACTIONr_scangle_other19.08819.8361240
X-RAY DIFFRACTIONr_lrange_it24.169240.5576650
X-RAY DIFFRACTIONr_lrange_other24.168240.5556650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.0270.425400.387740X-RAY DIFFRACTION99.872
3.027-3.1090.29280.406728X-RAY DIFFRACTION100
3.109-3.1990.376320.32715X-RAY DIFFRACTION100
3.199-3.2980.485290.304683X-RAY DIFFRACTION100
3.298-3.4060.335450.25664X-RAY DIFFRACTION100
3.406-3.5250.312390.223634X-RAY DIFFRACTION100
3.525-3.6580.199330.204624X-RAY DIFFRACTION100
3.658-3.8080.222320.194605X-RAY DIFFRACTION100
3.808-3.9770.309290.214578X-RAY DIFFRACTION100
3.977-4.170.297300.205560X-RAY DIFFRACTION100
4.17-4.3960.152260.155535X-RAY DIFFRACTION100
4.396-4.6620.155180.114511X-RAY DIFFRACTION100
4.662-4.9830.175240.116486X-RAY DIFFRACTION100
4.983-5.3820.188220.155444X-RAY DIFFRACTION100
5.382-5.8940.314250.222405X-RAY DIFFRACTION100
5.894-6.5870.311220.24387X-RAY DIFFRACTION100
6.587-7.6020.305130.203351X-RAY DIFFRACTION100
7.602-9.3010.241180.18293X-RAY DIFFRACTION99.6795
9.301-13.110.0990.174244X-RAY DIFFRACTION100
13.11-60.470.387140.296142X-RAY DIFFRACTION96.2963

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