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- PDB-4jvi: Crystal structure of PqsR co-inducer binding domain of Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 4jvi
TitleCrystal structure of PqsR co-inducer binding domain of Pseudomonas aeruginosa with inhibitor 3NH2-7Cl-C9QZN
ComponentsTranscriptional regulator MvfR
KeywordsTRANSCRIPTION REGULATOR/INHIBITOR / co-inducer binding / DNA / cytoplasmic / TRANSCRIPTION REGULATOR-INHIBITOR complex
Function / homology
Function and homology information


DNA-binding transcription factor activity
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-amino-7-chloro-2-nonylquinazolin-4(3H)-one / Transcriptional regulator MvfR / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsIlangovan, A. / Williams, P. / Emsley, J.
CitationJournal: Plos Pathog. / Year: 2013
Title: Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR).
Authors: Ilangovan, A. / Fletcher, M. / Rampioni, G. / Pustelny, C. / Rumbaugh, K. / Heeb, S. / Camara, M. / Truman, A. / Chhabra, S.R. / Emsley, J. / Williams, P.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Dec 4, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.d_res_high / _reflns_shell.d_res_low
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)24,6102
Polymers24,2881
Non-polymers3221
Water181
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2214
Polymers48,5772
Non-polymers6442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area2380 Å2
ΔGint-10 kcal/mol
Surface area18180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.441, 118.441, 115.409
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transcriptional regulator MvfR


Mass: 24288.475 Da / Num. of mol.: 1 / Fragment: co-inducer binding domain, UNP RESIDUES 94-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: UCBPP-PA14 / Gene: mvfR, PA14_51340, PqsR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q02IG8, UniProt: A0A0H2Z7A6*PLUS
#2: Chemical ChemComp-QZN / 3-amino-7-chloro-2-nonylquinazolin-4(3H)-one


Mass: 321.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H24ClN3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M Tri sodium citrate pH 6.0, 0.1M Ammonium acetate, 3% MPD , VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2010 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.9→38.36 Å / Num. all: 11633 / Num. obs: 11028 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 87.66 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.08 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9-2.981100
2.98-3.141100
3.14-3.18199.9
3.18-3.711100
3.71-4.11100
4.1-4.651100
4.65-5.51100
5.5-7.11100
7.1-12.3185.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 12.256 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26285 528 4.8 %RANDOM
Rwork0.2041 ---
obs0.20678 10483 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 101.404 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å23.2 Å20 Å2
2--3.2 Å20 Å2
3----10.37 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 22 1 1619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191649
X-RAY DIFFRACTIONr_angle_refined_deg2.0291.9822236
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0815202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05623.50677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.17515275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2081514
X-RAY DIFFRACTIONr_chiral_restr0.1360.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211239
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 32 -
Rwork0.364 762 -
obs--100 %

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