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- PDB-7nbw: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 7nbw
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with a pyridin agonist
ComponentsTranscriptional regulator MvfR
KeywordsDNA BINDING PROTEIN / QUORUM SENSING / LYSR-TYPE TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / 2 QUINOLONE SIGNALING SYSTEM / LTTR
Function / homology
Function and homology information


regulation of transmembrane transport / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding / extracellular region / plasma membrane
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-U7Q / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.28 Å
AuthorsSchmelz, S. / Blankenfeldt, W.
CitationJournal: Eur.J.Med.Chem. / Year: 2021
Title: Divergent synthesis and biological evaluation of 2-(trifluoromethyl)pyridines as virulence-attenuating inverse agonists targeting PqsR.
Authors: Schutz, C. / Hodzic, A. / Hamed, M. / Abdelsamie, A.S. / Kany, A.M. / Bauer, M. / Rohrig, T. / Schmelz, S. / Scrima, A. / Blankenfeldt, W. / Empting, M.
History
DepositionJan 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)25,9942
Polymers25,7001
Non-polymers2941
Water25214
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9894
Polymers51,4002
Non-polymers5882
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Unit cell
Length a, b, c (Å)121.386, 121.386, 114.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)

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Components

#1: Protein Transcriptional regulator MvfR


Mass: 25700.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 / Gene: mvfR, PA1003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X0
#2: Chemical ChemComp-U7Q / ~{N}-[3-(4-fluorophenyl)prop-2-ynyl]-2-(trifluoromethyl)pyridin-4-amine


Mass: 294.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10F4N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 4.75 Å3/Da / Density % sol: 74.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 198mM MgCl2 34.7% MPD 0.1M Tris pH 7.25 10mg/ml PqsR + 1.5 mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE 0.39 mM Amaranth (CAS 915-67-3) Cryo: + 20% 2,3- RR- Butandiol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.4769 Å
DetectorType: DECTRIS PILATUS3 X CdTe 2M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.4769 Å / Relative weight: 1
ReflectionResolution: 2.28→105.124 Å / Num. obs: 15066 / % possible obs: 95.9 % / Redundancy: 56.4 % / Biso Wilson estimate: 72.55 Å2 / CC1/2: 1 / Rpim(I) all: 0.016 / Net I/σ(I): 33.9
Reflection shellResolution: 2.28→2.5 Å / Mean I/σ(I) obs: 1.9 / Num. unique obs: 753 / CC1/2: 0.73 / Rpim(I) all: 0.667 / % possible all: 86.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.17 Å105.12 Å
Translation6.17 Å105.12 Å

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Processing

Software
NameVersionClassification
PHENIX1.19rc5_4047refinement
XDSdata reduction
STARANISOdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q7v

2q7v


Resolution: 2.28→25.62 Å / SU ML: 0.2831 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 39.0471
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2645 1500 9.98 %
Rwork0.2438 13527 -
obs0.2458 15027 64.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.33 Å2
Refinement stepCycle: LAST / Resolution: 2.28→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 0 21 14 1645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041661
X-RAY DIFFRACTIONf_angle_d0.94932252
X-RAY DIFFRACTIONf_chiral_restr0.0607257
X-RAY DIFFRACTIONf_plane_restr0.01290
X-RAY DIFFRACTIONf_dihedral_angle_d9.9421230
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.350.4267140.5773130X-RAY DIFFRACTION7.01
2.36-2.440.4975320.5466285X-RAY DIFFRACTION15.52
2.44-2.540.4058460.4698407X-RAY DIFFRACTION21.89
2.54-2.650.3714630.4085575X-RAY DIFFRACTION30.58
2.65-2.790.3986990.4093889X-RAY DIFFRACTION47.59
2.79-2.970.38091700.35231530X-RAY DIFFRACTION81.46
2.97-3.20.30872100.32751892X-RAY DIFFRACTION99.76
3.2-3.520.30792100.29691891X-RAY DIFFRACTION99.95
3.52-4.020.28082120.23721916X-RAY DIFFRACTION99.95
4.02-5.060.20982170.19011956X-RAY DIFFRACTION99.91
5.06-25.620.24542270.22012056X-RAY DIFFRACTION99.65
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)
12.833701866161.223397481150.857672625728.89378413515-0.2612595713355.40356833558-0.201622632019-0.089377733272-0.8065652127250.08777871338350.2365521772260.5987640920230.503393977947-0.0126354140499-0.00324831037980.367704452320.05680847792940.06432581693820.288309233447-0.1409958004010.549830229503-52.8346235179-20.1295540466-4.60426532496
23.62448634121-1.732084920230.8429147069624.9266604465-0.4788150076235.48199584014-0.1644940441340.4046303950330.140333360553-0.5494266443130.2630161635210.321095025482-1.02540226799-0.246196434814-0.1980921820610.76641269773-0.0115547374891-0.05313640892780.402932932732-0.1173741677750.399772512473-54.64567498050.780358664405-13.3215485962
33.72038223812-1.414293461490.891619042747.77004368606-1.267893811565.382556670.04000287343070.247195353118-0.266253961472-0.6276737219950.245976696398-0.267626180934-0.04785721718880.629984055502-0.2266402540640.39734529438-0.0288190310251-0.004839654395570.377246348788-0.2173548049070.374541119268-48.394121575-6.53361055556-10.5066860751
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 92 through 157 )92 - 1571 - 66
22chain 'A' and (resid 158 through 207 )158 - 20767 - 114
33chain 'A' and (resid 208 through 298 )208 - 298115 - 205

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