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- PDB-6q7u: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 6q7u
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with HHQ
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
2-heptyl-1~{H}-quinolin-4-one / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.14 Å
AuthorsWitzgall, F. / Xu, N. / 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)25,9432
Polymers25,7001
Non-polymers2431
Water1086
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8874
Polymers51,4002
Non-polymers4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area2320 Å2
ΔGint-7 kcal/mol
Surface area18190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.592, 116.592, 115.328
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-HLH / 2-heptyl-1~{H}-quinolin-4-one


Mass: 243.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 4.94 Å3/Da / Density % sol: 75.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 50% (v/v) ethylene glycol, 0.2 M MgCl2, 0.1 M CsCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: May 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 3.14→46.25 Å / Num. obs: 8549 / % possible obs: 99.8 % / Redundancy: 22.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.035 / Rrim(I) all: 0.164 / Net I/σ(I): 15.9 / Num. measured all: 192919
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.14-3.3624.32.1615010.770.4442.20599.6
8.88-46.2517.20.0514490.9990.0120.05399.2

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Processing

Software
NameVersionClassification
PHENIX1.14rc1_3177refinement
XDSXDSAPPdata reduction
Aimlessdata scaling
PDB_EXTRACT3.24data extraction
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4JVC

4jvc


Resolution: 3.14→46.249 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.89
RfactorNum. reflection% reflection
Rfree0.2711 458 5.38 %
Rwork0.2327 --
obs0.2349 8515 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 294.17 Å2 / Biso mean: 142.1381 Å2 / Biso min: 51.02 Å2
Refinement stepCycle: final / Resolution: 3.14→46.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 39 6 1628
Biso mean--109.15 98.09 -
Num. residues----204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1401-3.59440.36631470.2992599274699
3.5944-4.52790.27921390.245926582797100
4.5279-46.25360.24991720.212328002972100
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)
14.17611.8024-1.03583.447-2.51113.2034-0.18281.145-0.2841-0.54560.08110.08531.0398-0.2440.06850.9029-0.2558-0.02750.4271-0.1460.722374.743231.944312.6328
26.33281.50071.25754.2555-1.38693.3626-0.5193-0.90380.30560.7801-0.00670.63970.3486-0.01380.4681.1075-0.1195-0.030.7653-0.11050.837179.962740.365115.8547
34.3199-3.89573.34298.20060.53645.2482-0.41080.68230.509-0.0675-0.26-0.20870.16890.55430.35851.2166-0.2442-0.06711.21030.11550.882890.304847.67980.7641
43.6332-1.3011-0.99142.8082-1.89972.4443-0.65490.0282-1.6093-0.8726-0.1544-0.71442.4767-1.24771.00841.42910.07260.09811.949-0.19691.03298.646937.72281.5652
58.31922.76880.51884.653-0.63513.93660.939-0.53240.29771.4221-0.1740.24260.19540.1009-0.35381.1167-0.1998-0.08840.7884-0.13480.621180.754929.988522.2986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 93 through 137 )A93 - 137
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 173 )A138 - 173
3X-RAY DIFFRACTION3chain 'A' and (resid 174 through 242 )A174 - 242
4X-RAY DIFFRACTION4chain 'A' and (resid 243 through 262 )A243 - 262
5X-RAY DIFFRACTION5chain 'A' and (resid 263 through 296 )A263 - 296

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