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- PDB-6q7v: Crystal structure of PqsR (MvfR) ligand-binding domain in complex... -

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Basic information

Entry
Database: PDB / ID: 6q7v
TitleCrystal structure of PqsR (MvfR) ligand-binding domain in complex with compound 11
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-HLK / Multiple virulence factor regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.56 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator MvfR
B: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9714
Polymers51,4002
Non-polymers5702
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-4 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.380, 119.310, 114.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 94 through 107 or resid 109...
21(chain B and (resid 94 through 107 or resid 109...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNPHEPHE(chain A and (resid 94 through 107 or resid 109...AA94 - 1074 - 17
12ASPASPPHEPHE(chain A and (resid 94 through 107 or resid 109...AA109 - 11919 - 29
13ASNASNASNASN(chain A and (resid 94 through 107 or resid 109...AA12030
14ARGARGGLNGLN(chain A and (resid 94 through 107 or resid 109...AA93 - 2983 - 208
15ARGARGGLNGLN(chain A and (resid 94 through 107 or resid 109...AA93 - 2983 - 208
16ARGARGGLNGLN(chain A and (resid 94 through 107 or resid 109...AA93 - 2983 - 208
17ARGARGGLNGLN(chain A and (resid 94 through 107 or resid 109...AA93 - 2983 - 208
21ASNASNPHEPHE(chain B and (resid 94 through 107 or resid 109...BB94 - 1074 - 17
22ASPASPASNASN(chain B and (resid 94 through 107 or resid 109...BB109 - 12019 - 30
23METMETMETMET(chain B and (resid 94 through 107 or resid 109...BB12131
24ASNASNLEULEU(chain B and (resid 94 through 107 or resid 109...BB94 - 2954 - 205
25ASNASNLEULEU(chain B and (resid 94 through 107 or resid 109...BB94 - 2954 - 205
26ASNASNLEULEU(chain B and (resid 94 through 107 or resid 109...BB94 - 2954 - 205

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Components

#1: Protein Transcriptional regulator MvfR


Mass: 25700.068 Da / Num. of mol.: 2
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-HLK / ~{N}4-[(4-fluorophenyl)methyl]-6-(trifluoromethyl)pyridine-2,4-diamine


Mass: 285.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H11F4N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.03 Å3/Da / Density % sol: 69.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.1 M MES (pH 5.7), 0.1 M NaH2PO4, 0.1 M K2HPO4, 2.4 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→46.65 Å / Num. obs: 56181 / % possible obs: 84.5 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.073 / Rrim(I) all: 0.252 / Net I/σ(I): 6.1 / Num. measured all: 641266
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsRpim(I) allRrim(I) all% possible allCC1/2
1.83-1.871.21.3699411.3431.91923.2
8.96-46.6512.50.0226380.0060.02399.41

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Processing

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

4jvc


Resolution: 2.56→46.654 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 716 4.75 %
Rwork0.2148 14371 -
obs0.2162 15087 61.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 216.93 Å2 / Biso mean: 88.9846 Å2 / Biso min: 29.04 Å2
Refinement stepCycle: final / Resolution: 2.56→46.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 62 28 3220
Biso mean--77.2 49.33 -
Num. residues----408
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1786X-RAY DIFFRACTION8.393TORSIONAL
12B1786X-RAY DIFFRACTION8.393TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5596-2.75720.3497260.383849051611
2.7572-3.03460.4061720.35191263133528
3.0346-3.47360.30051270.2953157328468
3.4736-4.37590.24772530.218246524905100
4.3759-46.66190.22082380.185448095047100
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)
12.75663.1345-0.16125.886-1.01570.37670.0238-0.2578-0.68771.4927-0.4192-0.93910.6002-0.3545-0.54970.4198-0.01740.29180.5553-0.09320.6219-45.6496-36.095225.2046
22.5003-0.0432-0.99021.7594-1.32453.4282-0.32390.4145-0.69680.1047-0.12320.0387-0.0262-0.7887-0.13390.43510.02780.08310.3029-0.03510.4758-39.4037-32.208319.251
30.0570.0128-0.20330.8349-0.01670.4387-0.3022-0.11610.61671.534-0.19230.0199-0.4716-0.57760.00770.9646-0.149-0.40130.8030.17440.8127-18.603-15.603130.5251
40.37280.05120.21260.0004-0.07670.5369-0.88230.5055-1.24760.0139-0.0072-0.24860.90051.2698-0.02510.74930.05270.00250.83150.02360.6683-25.6118-32.359825.4664
51.0891-0.66210.76571.4258-0.26490.6992-0.4218-1.0432-0.01331.55930.4358-0.2929-0.45450.6991-0.04250.79770.0045-0.18940.45690.09060.5163-28.1763-27.357835.8261
60.41550.2034-0.02650.5521-0.54660.6927-0.4114-0.53390.35711.0626-0.2019-0.2583-0.82370.4555-0.00840.79760.0855-0.06960.54330.04210.5337-31.5782-20.703932.2975
70.7550.06870.8830.04710.24111.3756-0.2246-0.73930.83771.3564-0.24230.5176-0.6924-0.3329-0.67541.26010.0277-0.03770.5216-0.06280.6391-31.8866-12.513930.0469
80.39520.10710.00180.2938-0.25080.878-0.0281.09240.02970.325-0.10720.57490.3726-0.2972-0.00120.4912-0.00870.08580.7104-0.17050.5631-43.5379-31.030913.8604
93.96871.0021.01323.3281.32695.43750.0912-0.15530.83441.18650.06251.8842-0.9607-2.60921.1281.00110.35140.21981.19510.1990.6069-52.5365-24.361914.3971
102.34631.320.12541.2504-0.22340.9075-0.2434-0.0518-0.177-0.07250.2932-1.26090.20.4867-0.37040.26070.3174-0.10360.39050.22670.8537-20.2645-9.89322.3097
110.19940.04120.10140.7918-0.27191.1554-0.18430.102-0.17150.1710.2934-1.1420.060.32290.00560.36320.1642-0.0070.42510.05880.6831-21.2918-7.80382.5601
120.09650.1091-0.30380.1292-0.41871.36560.15370.8272-0.0467-0.4137-0.3048-1.15430.32030.0895-0.22460.37130.0798-0.03020.60840.30721.0947-12.7991-14.78624.8603
131.51980.50482.50020.24651.00364.4322-0.046-1.0211-0.45680.2995-0.1184-0.61030.5031-0.2773-0.33660.52390.1247-0.0490.4330.13710.651-22.4567-17.986211.8676
141.92780.38820.36960.99580.69840.7684-0.48021.13870.4929-0.5193-0.20291.24110.8919-0.5232-0.14660.606-0.13890.02740.8407-0.23560.5035-43.1958-27.7367-6.1115
150.82370.49440.78992.71660.3961.68790.09590.4934-0.53380.4791-0.1176-0.6680.952-0.3847-0.00980.8052-0.05790.12610.6719-0.11090.6609-31.3407-32.5721-2.0711
160.8730.80240.46470.72350.42040.7244-0.3550.8665-0.3112-1.2021-0.15330.28250.2264-0.7507-0.00370.5714-0.02630.10390.5914-0.05060.3903-35.9486-21.6805-8.5961
170.11730.3594-0.06991.7142-0.27940.0556-0.6520.19520.2593-0.798-0.03421.41910.0146-0.2733-0.40650.5130.0823-0.08450.9879-0.00380.4463-43.5169-23.04670.3365
183.8106-1.82491.9462.10081.52265.7175-0.1164-0.7795-0.28341.1865-0.2727-0.98370.68260.3058-3.12230.40920.0291-0.38840.47150.17960.6464-19.434-12.145713.5872
192.04021.12040.82931.9435-0.61711.18810.7012-0.51351.80771.3471-0.71920.6277-0.4425-0.62560.10710.66860.08840.0540.53290.05530.5025-28.5828-2.960112.555
201.77410.46881.42390.32440.36171.03220.382-0.2249-0.45950.0065-0.3163-0.24920.1499-0.7420.07990.47610.09350.20150.57-0.06630.4639-46.9382-32.702424.5271
210.1518-0.0254-0.0660.03620.090.02560.3185-1.27860.67881.29730.61430.6463-0.3607-1.23240.00271.18920.51430.06731.6181-0.09031.1483-54.838-26.844323.2354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 119 through 136 )B119 - 136
2X-RAY DIFFRACTION2chain 'B' and (resid 137 through 173 )B137 - 173
3X-RAY DIFFRACTION3chain 'B' and (resid 174 through 193 )B174 - 193
4X-RAY DIFFRACTION4chain 'B' and (resid 194 through 212 )B194 - 212
5X-RAY DIFFRACTION5chain 'B' and (resid 213 through 229 )B213 - 229
6X-RAY DIFFRACTION6chain 'B' and (resid 230 through 242 )B230 - 242
7X-RAY DIFFRACTION7chain 'B' and (resid 243 through 262 )B243 - 262
8X-RAY DIFFRACTION8chain 'B' and (resid 263 through 277 )B263 - 277
9X-RAY DIFFRACTION9chain 'B' and (resid 278 through 295 )B278 - 295
10X-RAY DIFFRACTION10chain 'A' and (resid 93 through 104 )A93 - 104
11X-RAY DIFFRACTION11chain 'A' and (resid 105 through 136 )A105 - 136
12X-RAY DIFFRACTION12chain 'A' and (resid 137 through 148 )A137 - 148
13X-RAY DIFFRACTION13chain 'A' and (resid 149 through 166 )A149 - 166
14X-RAY DIFFRACTION14chain 'A' and (resid 167 through 180 )A167 - 180
15X-RAY DIFFRACTION15chain 'A' and (resid 181 through 220 )A181 - 220
16X-RAY DIFFRACTION16chain 'A' and (resid 221 through 247 )A221 - 247
17X-RAY DIFFRACTION17chain 'A' and (resid 248 through 264 )A248 - 264
18X-RAY DIFFRACTION18chain 'A' and (resid 265 through 278 )A265 - 278
19X-RAY DIFFRACTION19chain 'A' and (resid 279 through 298 )A279 - 298
20X-RAY DIFFRACTION20chain 'B' and (resid 94 through 104 )B94 - 104
21X-RAY DIFFRACTION21chain 'B' and (resid 105 through 118 )B105 - 118

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