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- PDB-6q7w: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 6q7w
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 20
ComponentsTranscriptional regulator MvfR
KeywordsDNA BINDING PROTEIN / Quorum sensing / LysR-type transcriptional regulator / Pseudomonas 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
D-Maltodextrin-Binding Protein; domain 2 - #290 / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...D-Maltodextrin-Binding Protein; domain 2 - #290 / : / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HLQ / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.82 Å
AuthorsWitzgall, F. / Blankenfeldt, W.
CitationJournal: Chemmedchem / Year: 2020
Title: Flexible Fragment Growing Boosts Potency of Quorum-Sensing Inhibitors against Pseudomonas aeruginosa Virulence.
Authors: Zender, M. / Witzgall, F. / Kiefer, A. / Kirsch, B. / Maurer, C.K. / Kany, A.M. / Xu, N. / Schmelz, S. / Borger, C. / Blankenfeldt, W. / Empting, M.
History
DepositionDec 13, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)26,1984
Polymers25,7001
Non-polymers4973
Water46826
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3958
Polymers51,4002
Non-polymers9956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)121.218, 121.218, 114.555
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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 (bacteria) / Gene: mvfR, PA1003 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I4X0
#2: Chemical ChemComp-HLQ / ~{N}4-[3-(4-fluorophenyl)propyl]-6-(trifluoromethyl)pyridine-2,4-diamine


Mass: 313.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H15F4N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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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: 5.27 Å3/Da / Density % sol: 76.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.085 M tri-sodium citrate (pH 5.6), 29.8% (v/v) 2-methyl-2-propanol, 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.82→47.72 Å / Num. obs: 12501 / % possible obs: 99.9 % / Redundancy: 23.9 % / CC1/2: 1 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.026 / Rrim(I) all: 0.13 / Net I/σ(I): 28.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.82-2.9725.11.98317640.8420.4012.02399.8
8.92-47.7221.60.01747410.0040.01799.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.17data scaling
PHENIX1.14rc1_3177refinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JVC

4jvc


Resolution: 2.82→47.718 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 30.27
RfactorNum. reflection% reflection
Rfree0.262 644 5.17 %
Rwork0.2308 --
obs0.2325 12453 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 271.37 Å2 / Biso mean: 99.6726 Å2 / Biso min: 39.02 Å2
Refinement stepCycle: final / Resolution: 2.82→47.718 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1612 0 61 26 1699
Biso mean--94.81 77.06 -
Num. residues----205
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.82-3.03770.34581140.315323012415
3.0377-3.34340.33491270.288223022429
3.3434-3.8270.2911260.243923422468
3.827-4.82090.23121270.195823582485
4.8209-47.72510.24361500.222925062656
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)
14.22071.0215-0.91221.89850.27232.8491-0.35930.2677-0.3243-0.3602-0.05240.08061.07780.2684-0.05470.6854-0.0739-0.05080.5401-0.06160.732178.854132.07912.4891
23.6563.21810.63243.4733-0.94683.5072-0.1868-0.55960.85630.1297-0.22740.4446-0.15150.2685-0.0290.5386-0.0897-0.07640.4196-0.15110.648682.763241.08317.0543
33.90760.05130.60027.35151.03334.5277-0.74021.15260.4783-0.44020.51410.1413-0.04540.3344-0.00020.9421-0.2857-0.20980.9460.19350.679394.1950.23970.444
43.18451.2123-0.76252.21440.30990.7685-0.79361.2429-0.7201-1.03620.5219-0.24990.2630.4728-0.00060.8733-0.14280.05641.0283-0.07490.701299.697240.05220.7399
51.45440.09491.56372.98070.9141.88430.3414-1.06260.65270.563-0.44170.44890.02660.10180.00010.5675-0.1162-0.00130.6873-0.07520.678483.397937.249421.7896
61.2301-0.02810.35731.30280.05331.49940.5831-0.4251-2.0375-0.0172-0.8122-0.52250.54311.0172-0.02160.8909-0.0736-0.25430.92670.01011.018886.721425.381222.0307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 136 )A93 - 136
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 171 )A137 - 171
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 229 )A172 - 229
4X-RAY DIFFRACTION4chain 'A' and (resid 230 through 262 )A230 - 262
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 278 )A263 - 278
6X-RAY DIFFRACTION6chain 'A' and (resid 279 through 297 )A279 - 297

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