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- PDB-8q5l: PqsR coinducer binding domain of Pseudomonas aeruginosa with liga... -

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Basic information

Entry
Database: PDB / ID: 8q5l
TitlePqsR coinducer binding domain of Pseudomonas aeruginosa with ligand 2f: 2-(4-(3-((6-chloro-1-isopropyl-1H-benzo[d]imidazol-2-yl)amino)-2-hydroxypropoxy)phenyl)acetonitrile
ComponentsTranscriptional regulator MvfR
KeywordsTRANSCRIPTION / Transcriptional regulator
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-JVO / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMarkham-Lee, Z.J. / Emsley, J.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/N006615/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/K005138/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/N03371X/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/ N501852/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R012415/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X002950/1 United Kingdom
Wellcome Trust108876/B/15/Z United Kingdom
CitationJournal: J.Med.Chem. / Year: 2024
Title: Design, Synthesis, and Evaluation of New 1 H -Benzo[ d ]imidazole Based PqsR Inhibitors as Adjuvant Therapy for Pseudomonas aeruginosa Infections.
Authors: Soukarieh, F. / Mashabi, A. / Richardson, W. / Oton, E.V. / Romero, M. / Dubern, J.F. / Robertson, S.N. / Lucanto, S. / Markham-Lee, Z. / Sou, T. / Kukavica-Ibrulj, I. / Levesque, R.C. / ...Authors: Soukarieh, F. / Mashabi, A. / Richardson, W. / Oton, E.V. / Romero, M. / Dubern, J.F. / Robertson, S.N. / Lucanto, S. / Markham-Lee, Z. / Sou, T. / Kukavica-Ibrulj, I. / Levesque, R.C. / Bergstrom, C.A.S. / Halliday, N. / Kellam, B. / Emsley, J. / Heeb, S. / Williams, P. / Stocks, M.J. / Camara, M.
History
DepositionAug 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)24,6872
Polymers24,2881
Non-polymers3991
Water181
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3754
Polymers48,5772
Non-polymers7982
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
MethodPISA
Unit cell
Length a, b, c (Å)121.121, 121.121, 115.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcriptional regulator MvfR


Mass: 24288.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Gene: mvfR / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2Z7A6
#2: Chemical ChemComp-JVO / 2-[4-[(2~{S})-3-[(6-chloranyl-1-propan-2-yl-benzimidazol-2-yl)amino]-2-oxidanyl-propoxy]phenyl]ethanenitrile


Mass: 398.886 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 5.04 Å3/Da / Density % sol: 75.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Trisodium citrate (pH range 5.8-6.2), 0.2 M Ammonium acetate and MPD (3-8%)
PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.9→105.11 Å / Num. obs: 11410 / % possible obs: 98.1 % / Redundancy: 16.1 % / CC1/2: 0.998 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.1 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1602 / CC1/2: 0.653

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→105.11 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.927 / SU B: 16.033 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.4 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25003 547 4.8 %RANDOM
Rwork0.21983 ---
obs0.22132 10831 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 90.062 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å21.43 Å20 Å2
2--2.86 Å20 Å2
3----9.26 Å2
Refinement stepCycle: 1 / Resolution: 2.9→105.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 28 1 1627
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131658
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171539
X-RAY DIFFRACTIONr_angle_refined_deg1.391.6382251
X-RAY DIFFRACTIONr_angle_other_deg1.1281.5683555
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7345202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54921.30492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69715275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7771514
X-RAY DIFFRACTIONr_chiral_restr0.0520.2215
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021858
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it4.9289.563811
X-RAY DIFFRACTIONr_mcbond_other4.9169.554809
X-RAY DIFFRACTIONr_mcangle_it7.84414.3491012
X-RAY DIFFRACTIONr_mcangle_other7.83714.351012
X-RAY DIFFRACTIONr_scbond_it4.6149.967847
X-RAY DIFFRACTIONr_scbond_other4.6119.963848
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.56714.7461240
X-RAY DIFFRACTIONr_long_range_B_refined11.571752
X-RAY DIFFRACTIONr_long_range_B_other11.5671753
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 27 -
Rwork0.398 801 -
obs--100 %

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