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- PDB-6tpr: PqsR (MvfR) bound to inhibitory compound 40 -

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Basic information

Entry
Database: PDB / ID: 6tpr
TitlePqsR (MvfR) bound to inhibitory compound 40
ComponentsTranscriptional regulator MvfR
KeywordsDNA BINDING PROTEIN / Pseudomonas aeruginosa / Quorum sensing
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
D-Maltodextrin-Binding Protein; domain 2 - #290 / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NV5 / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsRichardson, W.K. / Emsley, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Front Chem / Year: 2020
Title: Hit Identification of New Potent PqsR Antagonists as Inhibitors of Quorum Sensing in Planktonic and Biofilm GrownPseudomonas aeruginosa.
Authors: Soukarieh, F. / Liu, R. / Romero, M. / Roberston, S.N. / Richardson, W. / Lucanto, S. / Oton, E.V. / Qudus, N.R. / Mashabi, A. / Grossman, S. / Ali, S. / Sou, T. / Kukavica-Ibrulj, I. / ...Authors: Soukarieh, F. / Liu, R. / Romero, M. / Roberston, S.N. / Richardson, W. / Lucanto, S. / Oton, E.V. / Qudus, N.R. / Mashabi, A. / Grossman, S. / Ali, S. / Sou, T. / Kukavica-Ibrulj, I. / Levesque, R.C. / Bergstrom, C.A.S. / Halliday, N. / Mistry, S.N. / Emsley, J. / Heeb, S. / Williams, P. / Camara, M. / Stocks, M.J.
History
DepositionDec 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0May 20, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Polymer sequence / Structure summary
Category: atom_site / citation ...atom_site / citation / entity_poly / pdbx_database_status / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_conf / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.auth_asym_id / _citation.country ..._atom_site.auth_asym_id / _citation.country / _citation.journal_id_ISSN / _entity_poly.pdbx_strand_id / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1May 27, 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
Revision 2.2Jan 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

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Assembly

Deposited unit
A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1922
Polymers26,7491
Non-polymers4421
Water362
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3834
Polymers53,4982
Non-polymers8852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area2180 Å2
ΔGint-4 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.754, 118.754, 115.242
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 UCBPP-PA14 (bacteria)
Gene: mvfR, PA14_51340 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2Z7A6
#2: Chemical ChemComp-NV5 / 2-[(5-methyl-[1,2,4]triazino[5,6-b]indol-3-yl)sulfanyl]-~{N}-(4-pyridin-2-yloxyphenyl)ethanamide


Mass: 442.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H18N6O2S / 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, sitting drop / pH: 6
Details: 100 mM Sodium citrate, 200 mM Ammonium acetate, 3% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 3.2→115.242 Å / Num. obs: 8390 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.98 / Rmerge(I) obs: 0.234 / Net I/σ(I): 6.6
Reflection shellResolution: 3.2→3.42 Å / Redundancy: 14 % / Rmerge(I) obs: 1.392 / Num. unique obs: 1466 / CC1/2: 0.982 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6q7w, 4jvc

6q7w

4jvc


Resolution: 3.2→115.24 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.939 / SU B: 20.575 / SU ML: 0.313 / Cross valid method: FREE R-VALUE / ESU R: 0.717 / ESU R Free: 0.357
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 413 4.942 %RANDOM
Rwork0.2066 ---
all0.208 ---
obs-8357 99.916 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 125.861 Å2
Baniso -1Baniso -2Baniso -3
1-4 Å22 Å20 Å2
2--4 Å20 Å2
3----12.976 Å2
Refinement stepCycle: LAST / Resolution: 3.2→115.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1594 0 32 2 1628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121660
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.6282256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3935202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.4521.42991
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.50315271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7921514
X-RAY DIFFRACTIONr_chiral_restr0.0850.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021293
X-RAY DIFFRACTIONr_nbd_refined0.2780.2815
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.268
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2720.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.23
X-RAY DIFFRACTIONr_mcbond_it8.35712.39811
X-RAY DIFFRACTIONr_mcangle_it13.16218.5621012
X-RAY DIFFRACTIONr_scbond_it8.85112.715848
X-RAY DIFFRACTIONr_scangle_it13.70118.8651244
X-RAY DIFFRACTIONr_lrange_it19.136169.9182555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.2830.333280.38565X-RAY DIFFRACTION99.6639
3.283-3.3730.449250.341564X-RAY DIFFRACTION100
3.373-3.4710.356290.313532X-RAY DIFFRACTION100
3.471-3.5780.306330.313519X-RAY DIFFRACTION100
3.578-3.6950.274330.281514X-RAY DIFFRACTION100
3.695-3.8250.332250.244493X-RAY DIFFRACTION100
3.825-3.9690.254310.237481X-RAY DIFFRACTION100
3.969-4.1310.231180.217466X-RAY DIFFRACTION100
4.131-4.3140.337210.191437X-RAY DIFFRACTION100
4.314-4.5240.258160.164442X-RAY DIFFRACTION100
4.524-4.7690.187160.125416X-RAY DIFFRACTION100
4.769-5.0570.164180.135390X-RAY DIFFRACTION100
5.057-5.4060.163140.157379X-RAY DIFFRACTION100
5.406-5.8380.2210.171335X-RAY DIFFRACTION100
5.838-6.3930.27140.203330X-RAY DIFFRACTION100
6.393-7.1450.29310.206280X-RAY DIFFRACTION100
7.145-8.2450.174130.192264X-RAY DIFFRACTION100
8.245-10.0860.114120.154226X-RAY DIFFRACTION100
10.086-14.2090.11870.157190X-RAY DIFFRACTION100
14.209-115.240.34580.381121X-RAY DIFFRACTION97.7273

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