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- PDB-7qa3: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 7qa3
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with compound N-((2-(4-phenoxyphenyl)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-A0F / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 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 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 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)75,3704
Polymers74,5152
Non-polymers8552
Water724
1
A: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6852
Polymers37,2571
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6852
Polymers37,2571
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.018, 122.610, 112.784
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-IDDetails
d_1ens_1(chain "A" and (resid 93 through 107 or resid 109...
d_2ens_1(chain "B" and (resid 93 through 107 or resid 109...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGPHEA1 - 15
d_12ens_1ASPPHEA17 - 149
d_13ens_1GLUGLNA151 - 206
d_21ens_1ARGPHEB1 - 15
d_22ens_1ASPPHEB17 - 149
d_23ens_1GLUGLNB151 - 206

NCS oper: (Code: givenMatrix: (-0.266808967544, -0.961001436899, -0.0727269765406), (-0.96132957045, 0.260035927236, 0.0907015629715), (-0.0682527055648, 0.0941145834889, -0.993219015806)Vector: -64. ...NCS oper: (Code: given
Matrix: (-0.266808967544, -0.961001436899, -0.0727269765406), (-0.96132957045, 0.260035927236, 0.0907015629715), (-0.0682527055648, 0.0941145834889, -0.993219015806)
Vector: -64.4563248551, -50.8624423595, 25.4805580694)

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Components

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


Mass: 37257.477 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-A0F / N-[[2-(4-phenoxyphenyl)-1,3-thiazol-5-yl]methyl]-2-(trifluoromethyl)pyridin-4-amine / N-((2-(4-phenoxyphenyl)thiazol-5-yl)methyl)-2-(trifluoromethyl)pyridin-4-amine


Mass: 427.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H16F3N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.7 M Sodium chloride 15 %(v/v) Glycerol 85 mM Sodium acetate pH 4.6 Protein: 7.5 mg/ml Compound: 1.5 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.67→112.8 Å / Num. obs: 14428 / % possible obs: 94 % / Redundancy: 13.3 % / Biso Wilson estimate: 65.32 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.032 / Net I/σ(I): 14.8
Reflection shellResolution: 2.67→2.67 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 710 / CC1/2: 0.732 / Rpim(I) all: 0.427

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
STARANISOdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7V

2q7v


Resolution: 2.67→53.86 Å / SU ML: 0.3192 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.3134
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 692 4.8 %
Rwork0.2084 13726 -
obs0.2102 14418 63.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.49 Å2
Refinement stepCycle: LAST / Resolution: 2.67→53.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3169 0 60 4 3233
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01243309
X-RAY DIFFRACTIONf_angle_d1.4584513
X-RAY DIFFRACTIONf_chiral_restr0.0658523
X-RAY DIFFRACTIONf_plane_restr0.0189582
X-RAY DIFFRACTIONf_dihedral_angle_d10.3121468
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.34657436019 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.880.4071190.3453436X-RAY DIFFRACTION10.2
2.88-3.170.3804630.32421303X-RAY DIFFRACTION30.7
3.17-3.620.32661440.26143271X-RAY DIFFRACTION75.89
3.62-4.560.23932080.19564299X-RAY DIFFRACTION99.87
4.56-53.860.21872580.18754417X-RAY DIFFRACTION99.89
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)
11.80140569178-0.2153454093-0.6104247640712.85036670623-0.7929056641112.74046852335-0.5594165678790.340006300833-0.0154949576852-0.2387965905120.199437011737-1.0125523693-0.1900132193990.5808039282830.1256110934150.1222853688170.108138704488-0.01090612938270.3394609848890.1817812454330.529353544522-20.1996714509-9.854864501743.01877288466
29.969757805471.88750839061.063456820090.7409291454811.029588577831.88630665880.2060998431780.229519432922-1.135998696810.636462891583-1.08611298479-1.423417927110.4868591408390.621241443183-0.1729564489220.656696074197-0.0737423854055-0.1267456076110.3870171924260.3833682240810.515993794993-20.3177032128-19.730231111712.337100742
33.062784965551.893011498011.75375756653.431333750541.116949925173.657770463350.1169019075770.10244598433-0.148111336562-0.243408217315-0.267614554771-0.01171377088490.0584015784456-0.9013128164290.170236157080.2458300944430.01032575413560.03339983067010.452122447147-0.05986203243090.181428259014-41.6048112491-24.0114959025-2.16165329586
44.18759937804-0.232819083512-2.433993134033.98021512995-1.743005771743.69236595491-0.2773410541751.22059202617-0.0439345915706-0.343222175587-0.2531947648290.6159604030650.582102582974-0.577582062256-0.465707645830.546042217172-0.4622102985020.5294575962340.7940838620860.04937469789250.159779552676-42.9995299381-35.8760186534-1.86812377797
52.112970472130.7177007859640.5616254280662.87519736081-1.491074218673.3172769036-0.4163028542640.996688722851-0.5285407385780.769416969322-0.016049013356-1.394665156690.03244942016210.576276920498-0.1760041898370.6666471321160.06956856956520.07638127045070.454745958831-0.1179156431040.626693201253-27.5471190247-31.2532332621-2.62808539116
61.759452259031.706184296910.890750926551.629546593561.0582326871.87679256181-0.2852481361080.918550378989-0.0130340508978-0.719740580560.06911526429040.0343059719274-0.372308230898-0.421154227585-0.04332941958490.5451046125770.03310987012340.05190978120320.517743428603-0.05066888269670.27770445371-36.9889282969-21.4241821014-8.89019129052
73.652464616720.8903942091490.09957546605286.765653799093.997145674053.18798039103-0.306924934743-0.00530648095375-0.5085807043-0.5213194048920.2128695694720.92211926663-0.46218227547-0.7395597851540.106302497360.237801168230.0823260310339-0.03313622892650.5876309789730.06584045583080.353819930961-45.517185208-23.002278309-1.12302552287
82.12849977202-0.3331020192421.081852062661.332973007390.8674083286823.32480933589-0.111785744021-0.970165773048-0.3365114648010.375568047480.0326489975824-0.6671360195390.2298871024190.281980076853-0.08921410382550.3475371951310.108090522563-0.09673508754260.3419748653960.07626020815290.397504035248-22.6795962086-13.206195349912.6700566188
99.725040157281.419865510891.478797144755.4924088876-0.8192928511265.508336186141.0234429312-0.4940373015491.366582609041.0225140864-0.6722973005070.742410904459-0.0652444707812-0.220181545738-0.227245722650.71180091258-0.03909663636180.03243707442370.4062373103510.07960170930320.400109212721-29.2026296581-2.8412188150712.7954267233
104.78281790522.31225885558-0.1532499212784.691989497871.08634681743.031961448370.525095559706-0.3529011106350.2478496083490.317394089261-0.5915140111610.444115161635-0.163369938016-0.952504107414-0.01120160493730.436776044240.0638208655070.06916839559730.5112916403760.02306950965710.339962114532-50.7839907831-32.452346894523.7077966838
114.126675872670.0045561214734-1.016649607113.15783668568-0.7310614402243.5169117878-0.1723639951340.633516300115-0.3233790949240.2530102505130.23304986021-0.441791730131-0.142674855862-0.0815564343006-0.102186074590.2788817360320.0987753428533-0.05066895371630.1831522763770.01273016504610.353694403978-36.284037111-27.290086233221.585461362
126.045073370220.6539624629681.862609289143.70388895335-2.77033807555.87995216590.261895006262-0.451883428498-0.3169412026660.806444514223-0.3932820718-0.106087865474-0.5009988188370.1903970204610.04683826751380.538603762069-0.0301808043029-0.04715419123930.3848194457590.06367291879070.236510432022-28.8586388115-24.089700746330.107241659
136.043054312520.4246234378880.818996591432.24398551722-1.269397308713.08242633562-0.2609652152840.7896745249550.239218416528-0.220880580840.4773238465330.861267519593-0.0773841604832-0.403480077631-0.2101619151950.534856383832-0.1053074832270.09625434054550.564963731115-0.07197589946380.326357009924-50.5161973798-26.054004035514.4381488653
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 148 )AA93 - 1481 - 56
22chain 'A' and (resid 149 through 161 )AA149 - 16157 - 69
33chain 'A' and (resid 162 through 181 )AA162 - 18170 - 89
44chain 'A' and (resid 182 through 193 )AA182 - 19390 - 101
55chain 'A' and (resid 194 through 220 )AA194 - 220102 - 128
66chain 'A' and (resid 221 through 247 )AA221 - 247129 - 155
77chain 'A' and (resid 248 through 262 )AA248 - 262156 - 170
88chain 'A' and (resid 263 through 278 )AA263 - 278171 - 186
99chain 'A' and (resid 279 through 298 )AA279 - 298187 - 206
1010chain 'B' and (resid 93 through 137 )BB93 - 1371 - 45
1111chain 'B' and (resid 138 through 185 )BB138 - 18546 - 93
1212chain 'B' and (resid 186 through 262 )BB186 - 26294 - 170
1313chain 'B' and (resid 263 through 298 )BB263 - 298171 - 206

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