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- PDB-4jvc: Crystal structure of PqsR co-inducer binding domain -

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Basic information

Entry
Database: PDB / ID: 4jvc
TitleCrystal structure of PqsR co-inducer binding domain
ComponentsTranscriptional regulator MvfR
KeywordsTRANSCRIPTION REGULATOR / transcription regulation / co-inducer binding / DNA binding
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
Transcriptional regulator MvfR / Transcriptional regulator MvfR
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.5 Å
AuthorsIlangovan, A. / Emsley, J. / Williams, P.
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 1.2Mar 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)24,5253
Polymers24,2881
Non-polymers2362
Water543
1
A: Transcriptional regulator MvfR
hetero molecules

A: Transcriptional regulator MvfR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0506
Polymers48,5772
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area2510 Å2
ΔGint-6 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.733, 119.733, 115.777
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-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 4.93 Å3/Da / Density % sol: 75.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Ammonium acetate, 0.1M Tri sodium citrate pH 6.5, 3% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: GRAPHITE / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 19299 / Num. obs: 17339 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Biso Wilson estimate: 71.9 Å2 / Rmerge(I) obs: 0.74 / Rsym value: 0.85 / Net I/σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.5-2.66199.9
2.66-2.78199.8
2.78-2.92199.9
2.92-3.091100
3.09-3.291100
3.29-3.54199.8
3.54-3.841100
3.84-4.251100
4.25-4.821100
4.82-5.7199.8
5.7-7.361100
7.36-12.75199.6

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→28.98 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.112 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26711 874 5.1 %RANDOM
Rwork0.2218 ---
obs0.22399 16426 98.91 %-
all-1 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 99.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20.25 Å20 Å2
2--0.25 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 16 3 1617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191642
X-RAY DIFFRACTIONr_bond_other_d0.0010.021585
X-RAY DIFFRACTIONr_angle_refined_deg2.171.9782230
X-RAY DIFFRACTIONr_angle_other_deg0.99133628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5175202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61323.50677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.10415275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531514
X-RAY DIFFRACTIONr_chiral_restr0.1230.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02381
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.553 69 -
Rwork0.514 1166 -
obs--99.84 %

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