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

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Basic information

Entry
Database: PDB / ID: 7qav
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with compound N-((2-(4-cyclopropylphenyl)thiazol-5-yl)methyl)-2-(trifluoromethyl)pyridin-4-amine
ComponentsMultiple virulence factor 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-XBH / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSchmelz, S. / Blankenfeldt, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Ssrn / Year: 2024
Title: Discovery and Optimization of Thiazole-Based Quorum Sensing Inhibitors as Potent Blockers of Pseudomonas Aeruginosa Pathogenicity
Authors: Abdelsamie, A.S. / Hamed, M.M. / Schutz, C. / Rohrig, T. / Kany, A.M. / Schmelz, S. / Blankenfeldt, W. / Hirsch, A.K.H. / Hartmann, R.W. / Empting, M.
History
DepositionNov 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 12, 2024Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multiple virulence factor regulator MvfR
B: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2644
Polymers74,5132
Non-polymers7512
Water18010
1
A: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6322
Polymers37,2561
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6322
Polymers37,2561
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.728, 121.152, 112.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
d11
d21

NCS oper: (Code: givenMatrix: (-0.200549570896, -0.976770325262, -0.0754957038608), (-0.976040428943, 0.192570052196, 0.101300819673), (-0.0844094229483, 0.0940026950965, -0.991987168582)Vector: -61. ...NCS oper: (Code: given
Matrix: (-0.200549570896, -0.976770325262, -0.0754957038608), (-0.976040428943, 0.192570052196, 0.101300819673), (-0.0844094229483, 0.0940026950965, -0.991987168582)
Vector: -61.072088022, -51.6695255219, 25.0418706376)

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Components

#1: Protein Multiple virulence factor regulator MvfR / Transcriptional regulator MvfR


Mass: 37256.492 Da / Num. of mol.: 2
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-XBH / ~{N}-[[2-(4-cyclopropylphenyl)-1,3-thiazol-5-yl]methyl]-2-(trifluoromethyl)pyridin-4-amine


Mass: 375.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16F3N3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.48 Å3/Da / Density % sol: 50.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.860 M LiCl 155 mM MgCl2 0.1 M MES pH 6.1 Protein: 6.5 mg/ml Compound: 2 mM Cryoprotectant: 20% 2,3-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9537 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.65→80.9 Å / Num. obs: 10629 / % possible obs: 91.2 % / Redundancy: 7.2 % / Biso Wilson estimate: 56.32 Å2 / CC1/2: 0.998 / Net I/av σ(I): 10.2 / Net I/σ(I): 0.048
Reflection shellResolution: 2.65→2.94 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 531 / CC1/2: 0.563 / Rpim(I) all: 0.487

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7V

2q7v


Resolution: 2.65→53.29 Å / SU ML: 0.2113 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.9162
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2868 512 4.82 %
Rwork0.2476 10107 -
obs0.2496 10619 48.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.69 Å2
Refinement stepCycle: LAST / Resolution: 2.65→53.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3065 0 52 10 3127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01393178
X-RAY DIFFRACTIONf_angle_d2.17244336
X-RAY DIFFRACTIONf_chiral_restr0.1229512
X-RAY DIFFRACTIONf_plane_restr0.0128597
X-RAY DIFFRACTIONf_dihedral_angle_d5.175480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.920.5073160.4279438X-RAY DIFFRACTION8.42
2.92-3.340.4319580.36761186X-RAY DIFFRACTION23.04
3.34-4.20.30151920.26523111X-RAY DIFFRACTION60.44
4.2-53.290.26032460.2275372X-RAY DIFFRACTION99.8
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)
16.201949325671.634903270360.9899414550666.029190036710.519687745155.713966214870.03957700080150.222124955929-0.347560033253-0.327748604842-0.0201635689436-0.366532736599-0.25655316710.3310410186810.02911571093560.3498986907610.08454126120740.07508147385690.340000229520.04539674419510.246874986714-20.1826973815-10.25785931181.89640755822
22.879061165240.6852310249480.5121455966022.43887164823-0.1588464081013.60345281786-0.03276821006970.125244713769-0.395479168279-0.1129754078690.0606400077856-0.4013802284030.197985857811-0.0171648359271-0.04268640842380.3285041133460.1834972472640.1162644950850.156146335860.001054938732730.0582372995812-24.3377222068-15.13700054833.37828583462
31.152942398980.083189711651-0.5275299797861.372440013261.203526227582.33004140569-0.2802819263680.0434889060342-0.2907996987570.2186722193160.1067212084750.05942563459450.627523745139-0.336963078408-0.2767863380370.818221255447-0.1016096835290.1522316647850.462278953517-0.2419157188890.177187157183-34.1838599399-33.20665367-1.29930873214
41.310074112930.4237441671250.2217180590792.883230481911.332005480713.91055949896-0.388243973390.598073029336-0.302269654298-0.26833526930.12380517576-0.1993196193230.176247540569-0.372155599782-0.06269349305380.440572015604-0.06239170267990.1136677153590.478945731501-0.06580314847310.0471883496112-34.1550911172-22.8246611028-8.91664912947
50.8650400754770.760970081603-0.4916439309873.02355339742-0.8346551750282.158453577810.176691270644-0.1217398191160.1965338601330.324068871902-0.0832182066162-0.00749966491095-0.44221470571-0.2426177311510.09406054030370.4556221329260.2658777648880.0003808058164650.3637688087760.0672647520852-0.0162529340124-30.1909176819-12.03422775199.05043970711
65.009622301761.65832898792-0.7657758810051.9627683549-0.6691078096433.26799905818-0.1764782868470.206364146533-0.1729745739730.03035345808440.02446027817740.1330068782-0.203238344594-0.8046009345870.1454009078630.2907351726910.02600296657180.153331078110.567354540593-0.01295779385080.0419098687222-45.8497731397-35.209260708721.628949471
70.634608660975-0.319962561552-0.03638307705240.849747464995-1.359651353562.76310247493-0.2388770930020.1248610482430.294987224060.259691207252-0.0483805276672-0.149678462054-1.066023894490.4861405412720.307522933640.8085180018720.1028719393420.01944648970450.5070607234130.07576301790.0572426682614-28.6551841083-19.064553968825.2970901525
84.97034279461-0.7975203815490.5459814417893.44557275475-2.241829552164.67387409990.2347055766880.0856529316007-0.2123447058720.324119124078-0.340218323492-0.06806563707710.2185537449020.648378909320.06094933010050.461732343733-0.2379353773620.07058223795970.4507088096720.01464507580450.0143365698773-28.114835276-26.08972947831.0610742362
91.041819940880.317126057932-0.2882405469261.979740911110.06683592965892.370521608760.200767767928-0.008691937226050.1834496995350.206437850811-0.2559755775950.468488814509-0.39297168473-1.07117196680.0317349741920.3163757603450.112789275712-0.01363190635650.4395074298180.035097125214-0.0860182783328-43.3926778946-23.434352330817.8639368149
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 93 through 104 )AA93 - 1041 - 12
22chain 'A' and (resid 105 through 180 )AA105 - 18013 - 88
33chain 'A' and (resid 181 through 214 )AA181 - 21489 - 120
44chain 'A' and (resid 215 through 247 )AA215 - 247121 - 153
55chain 'A' and (resid 248 through 297 )AA248 - 297154 - 203
66chain 'B' and (resid 93 through 157 )BC93 - 1571 - 64
77chain 'B' and (resid 158 through 190 )BC158 - 19065 - 97
88chain 'B' and (resid 191 through 247 )BC191 - 24798 - 154
99chain 'B' and (resid 248 through 296 )BC248 - 296155 - 203

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