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- PDB-7p4u: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 7p4u
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE
ComponentsTranscriptional regulator MvfR
KeywordsGENE REGULATION / QUORUM SENSING / LYSR-TYPE TRANSCRIPTIONAL REGULATOR / PSEUDOMONAS / 2 QUINOLONE SIGNALING SYSTEM / LTTR / DNA BINDING PROTEIN
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-5N9 / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å
AuthorsSchmelz, S. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2023
Title: Towards Translation of PqsR Inverse Agonists: From In Vitro Efficacy Optimization to In Vivo Proof-of-Principle.
Authors: Hamed, M.M. / Abdelsamie, A.S. / Rox, K. / Schutz, C. / Kany, A.M. / Rohrig, T. / Schmelz, S. / Blankenfeldt, W. / Arce-Rodriguez, A. / Borrero-de Acuna, J.M. / Jahn, D. / Rademacher, J. / ...Authors: Hamed, M.M. / Abdelsamie, A.S. / Rox, K. / Schutz, C. / Kany, A.M. / Rohrig, T. / Schmelz, S. / Blankenfeldt, W. / Arce-Rodriguez, A. / Borrero-de Acuna, J.M. / Jahn, D. / Rademacher, J. / Ringshausen, F.C. / Cramer, N. / Tummler, B. / Hirsch, A.K.H. / Hartmann, R.W. / Empting, M.
History
DepositionJul 13, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 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)26,1232
Polymers25,7001
Non-polymers4231
Water1267
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2464
Polymers51,4002
Non-polymers8462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area1300 Å2
ΔGint-10 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.319, 120.319, 115.201
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)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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 (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: mvfR, PA1003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X0
#2: Chemical ChemComp-5N9 / ~{N}-[[2-(3-chloranyl-4-propan-2-yloxy-phenyl)pyrimidin-5-yl]methyl]-2-(trifluoromethyl)pyridin-4-amine


Mass: 422.831 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18ClF3N4O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 5.26 Å3/Da / Density % sol: 76.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% MPD, 30mM magnesium formate,120 mM Lithium citrate, 100mM MES pH 5.6, 10mg/ml PqsR + 1mM 3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE Cryo: + 20% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.74→104.199 Å / Num. obs: 9271 / % possible obs: 95.2 % / Redundancy: 36.2 % / Biso Wilson estimate: 90.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.09 / Net I/σ(I): 32.6
Reflection shellResolution: 2.74→2.985 Å / Rmerge(I) obs: 3.587 / Num. unique obs: 464 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
AutoProcessdata reduction
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q7v

2q7v


Resolution: 2.74→60.16 Å / SU ML: 0.3015 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 38.1152
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2749 463 5 %
Rwork0.2461 8804 -
obs0.2476 9267 69.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.45 Å2
Refinement stepCycle: LAST / Resolution: 2.74→60.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 29 7 1589
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541613
X-RAY DIFFRACTIONf_angle_d0.80632200
X-RAY DIFFRACTIONf_chiral_restr0.0557257
X-RAY DIFFRACTIONf_plane_restr0.0105282
X-RAY DIFFRACTIONf_dihedral_angle_d7.2364225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.74-3.140.3408550.3558916X-RAY DIFFRACTION22.34
3.14-3.950.32211690.29613477X-RAY DIFFRACTION82.81
3.96-60.160.25872390.22524411X-RAY DIFFRACTION99.96
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)
12.10852580380.0163993534951-0.5116977240819.374585250890.4978656502474.42183193514-0.192620862274-0.264426122193-0.1237584720880.6216636402080.01063626399310.7015672229660.1684050018980.317106464490.1647816144540.2796846227630.01853093802440.04876564838120.40931198035-0.1407433304320.362584433538-51.2970073694-17.0825719567-4.56487302367
28.62251430581-4.31821509024-1.150596490824.24186728233-0.128061584377.409212093120.0534607314325-0.0989187055890.496420300542-0.238107216891-0.2916274415380.480770061516-1.057676624990.07660751759430.3246146877530.9060420473280.0225552682853-0.2304205082620.403184340804-0.0812976689340.284066694826-57.7811031262.83213963352-17.403602721
32.71088335915-0.1644721246671.456715164958.79659886346-0.07685626367544.399379807090.01706113507540.164918399936-0.0228027875972-0.161667701212-0.105659355084-0.6164770873460.02766247535650.9293888101860.07145111264150.2212422431920.0458630361040.02508906405230.422317524015-0.2048679647930.304644759126-45.5779824168-7.33937131179-9.45364359409
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 93 through 171 )93 - 1711 - 79
22chain 'A' and (resid 172 through 220 )172 - 22080 - 128
33chain 'A' and (resid 221 through 296 )221 - 296129 - 204

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