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- PDB-7qa0: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 7qa0
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 1456
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-9ZL / 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)75,3714
Polymers74,5152
Non-polymers8562
Water1267
1
A: Multiple virulence factor regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6852
Polymers37,2571
Non-polymers4281
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-polymers4281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.131, 119.824, 114.033
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 95 or (resid 96...
d_2ens_1(chain "B" and (resid 93 through 152 or (resid 153...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ARGSERA1 - 107
d_12ens_1ASNPHEA114 - 149
d_13ens_1GLUARGA151 - 205
d_21ens_1ARGPHEB1 - 143
d_22ens_1GLUARGB145 - 199

NCS oper: (Code: givenMatrix: (-0.239074388623, -0.967483884886, -0.0825734169725), (-0.967745331891, 0.230451389557, 0.101789634322), (-0.0794506721729, 0.104245333407, -0.991373038343)Vector: -61. ...NCS oper: (Code: given
Matrix: (-0.239074388623, -0.967483884886, -0.0825734169725), (-0.967745331891, 0.230451389557, 0.101789634322), (-0.0794506721729, 0.104245333407, -0.991373038343)
Vector: -61.6998989668, -50.2557962088, 25.8316733819)

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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-9ZL / ~{N}-[[2-(3-chloranyl-4-propan-2-yloxy-phenyl)-1,3-thiazol-5-yl]methyl]-2-(trifluoromethyl)pyridin-4-amine


Mass: 427.871 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H17ClF3N3OS / 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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.5 M LiCl 125 mM MgAcet 0.1 M MES pH 6.6 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: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.67→60.1 Å / Num. obs: 10949 / % possible obs: 93.3 % / Redundancy: 12.9 % / Biso Wilson estimate: 71.18 Å2 / CC1/2: 1 / Rpim(I) all: 0.029 / Net I/σ(I): 15.3
Reflection shellResolution: 2.67→2.96 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 547 / CC1/2: 0.43 / Rpim(I) all: 0.58

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROC20190301data processing
STARANISOdata scaling
PHENIXphasing
autoPROC20190301data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q7V

2q7v


Resolution: 2.67→54.57 Å / SU ML: 0.2363 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.8523
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2809 497 4.54 %
Rwork0.2364 10446 -
obs0.2385 10943 50.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.3 Å2
Refinement stepCycle: LAST / Resolution: 2.67→54.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 56 7 3141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753201
X-RAY DIFFRACTIONf_angle_d0.96954371
X-RAY DIFFRACTIONf_chiral_restr0.0578513
X-RAY DIFFRACTIONf_plane_restr0.009560
X-RAY DIFFRACTIONf_dihedral_angle_d8.8118445
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.4887577927 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.940.5922230.4519467X-RAY DIFFRACTION9.24
2.94-3.370.3289490.34391248X-RAY DIFFRACTION24.28
3.37-4.240.31341690.25823460X-RAY DIFFRACTION67.52
4.24-54.570.26042560.21655271X-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)
11.705338282360.1528203991880.7853570252411.581771990560.06026048690121.30876630192-0.1116515346360.05344222957310.09965341870240.0977384925136-0.0535929605714-0.6092821682610.01350378989490.279413459027-0.226443310377-0.1111293301530.3866221682760.0839679763040.01684069066630.0752644427530.292724889223-18.995903907-9.818846471053.03865976441
22.538183968121.411765823260.5950309761232.662299780791.028425102622.53370634405-0.2096772138830.122544189341-0.6143461600580.06997370786180.13699839954-0.3163527490360.430708490351-0.358584536990.008626938812290.294269251030.0021861031890.09729490097060.1295990072310.1260129296130.194474408002-32.9895563539-26.71861813271.16824941441
31.340703328021.73858608717-0.147516532473.89905742415-2.602830747083.577801216610.0651536868315-0.330996028189-0.2611531023740.505963913409-0.0774419138868-0.6162623505050.1069534158590.156822600420.1215523630760.720309750409-0.08404732732480.2618149753570.505430599491-0.04065297061870.499811970987-27.0234768103-31.0869022412-1.84943436975
40.3855712239320.445122484753-0.3708972132761.561445262650.06958019709850.992436938787-0.129920285810.34837532620.08815678904370.1125806486370.285228024796-0.0132943123992-0.430122522149-0.12055580031-0.01021425711310.1498253361660.0584682020459-0.06878627421660.3501752701340.0782701469216-0.0156727544689-32.3815559433-15.17093708882.62604683219
52.920943433390.57709433804-0.8396686566480.78321983647-0.07929396904371.745525728680.19869743436-0.116435717970.487348889310.0159317497489-0.2611134205760.378521620756-0.267570221218-0.838342434888-0.1199391818690.4700213818540.1020848247710.3327368639970.890752465899-0.08431697931520.357287529063-51.6038352684-29.070672488723.7655496783
61.945552783120.672817762711-1.152786240770.6461862758140.005064689870641.200926112150.06363664118540.2568837229810.0211450099784-0.0572472765582-0.09798309644340.08418109785150.0331058280625-0.6445234106310.06354510093640.0990294956833-0.08812763730460.3528586151740.740214055953-0.1941886266740.145133359744-45.4436340505-36.641867688624.4145071712
70.34920680896-0.161829699099-0.05767728264890.892409862835-0.410845030181.97048898889-0.2564737686540.144783403795-0.05687501434270.3241537132660.146745917113-0.183064712073-0.18860191250.0603753138252-0.1250604018330.277345537460.02373709894650.1331372576030.241267175324-0.170473274705-0.29041048321-36.1458998365-28.789727450821.4945403977
82.256114683511.44187930633-0.3218959056321.51732283996-0.811833103221.55467033268-0.026588641830.2282458351790.2678095125820.150560043247-0.330445090663-0.59560856132-0.5144353992740.5141939511420.174334303460.567850440742-0.0511963325027-0.3230812979240.8092077060820.2613860337140.524334175143-20.6304121127-23.971326115426.0524224038
90.799145829027-0.6996151436470.7839716231850.849552324704-1.04143704762.12680380284-0.01884419009610.003331032009250.1009534856780.124202787449-0.152911956321-0.178803853485-0.1603223982270.2601466336030.1365491118850.67178580692-0.104853150544-0.5344006343090.09831488677670.444056941642-0.00317042016194-28.5946419085-27.235547992536.6823308894
100.7088303036280.0650164207683-0.001828222749361.21293698131-0.9156387729440.6916895750160.1707259137-0.190690536220.2021456608910.67359722268-0.177827881033-0.0698494503012-0.3997987394710.00408568067444-0.06172450374691.08655513533-0.0256342674516-0.0658475727060.1980450603510.03244043360340.151836374527-32.0187731525-15.745799742529.3712757068
112.87092952235-1.49106309096-0.7547849110793.69117540816-2.100889090563.38957407130.3863753840310.280890706557-0.0678744034056-0.594758265522-0.202348939460.7441491473690.0710443512163-1.387150751150.1140070300280.3260578739950.164008173391-0.03611373886320.916513808132-0.140037770490.168465409099-49.4911586489-27.437464541414.1565620185
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 202 )AA149 - 20257 - 110
33chain 'A' and (resid 203 through 220 )AA203 - 220111 - 128
44chain 'A' and (resid 221 through 298 )AA221 - 298129 - 206
55chain 'B' and (resid 93 through 118 )BB93 - 1181 - 26
66chain 'B' and (resid 119 through 137 )BB119 - 13727 - 45
77chain 'B' and (resid 138 through 180 )BB138 - 18046 - 88
88chain 'B' and (resid 181 through 214 )BB181 - 21489 - 116
99chain 'B' and (resid 215 through 233 )BB215 - 233117 - 135
1010chain 'B' and (resid 234 through 264 )BB234 - 264136 - 166
1111chain 'B' and (resid 265 through 297 )BB265 - 297167 - 199

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