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- PDB-5uic: Structure of the Francisella response regulator receiver domain, QseB -

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Basic information

Entry
Database: PDB / ID: 5uic
TitleStructure of the Francisella response regulator receiver domain, QseB
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / Francisella / response regulator / QseB / biofilm / two component system
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain profile. / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Two-component response regulator
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.487 Å
AuthorsAllen, C.L. / Milton, M.E. / Cavanagh, J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM55769 United States
Department of Health & Human Services (HHS)HHSN272201500010C United States
CitationJournal: Mol. Microbiol. / Year: 2017
Title: Structure of the Francisella response regulator QseB receiver domain, and characterization of QseB inhibition by antibiofilm 2-aminoimidazole-based compounds.
Authors: Milton, M.E. / Allen, C.L. / Feldmann, E.A. / Bobay, B.G. / Jung, D.K. / Stephens, M.D. / Melander, R.J. / Theisen, K.E. / Zeng, D. / Thompson, R.J. / Melander, C. / Cavanagh, J.
History
DepositionJan 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: 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: Two-component response regulator
B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)31,5732
Polymers31,5732
Non-polymers00
Water72140
1
A: Two-component response regulator

B: Two-component response regulator


Theoretical massNumber of molelcules
Total (without water)31,5732
Polymers31,5732
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554y+1/2,-x+1/2,z-1/41
Buried area1820 Å2
ΔGint-10 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.737, 47.737, 191.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Two-component response regulator


Mass: 15786.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida (strain U112) (bacteria)
Strain: U112 / Gene: FTN_1465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0Q7W8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 1.73 Å3/Da / Density % sol: 28.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1 M potassium citrate, 0.1 M glycine, and 0.05 M bis-tris propane (BTP) pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.487→38.25 Å / Num. obs: 8414 / % possible obs: 99.6 % / Redundancy: 18.1 % / Biso Wilson estimate: 55.1 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.03 / Rrim(I) all: 0.12 / Χ2: 2.811 / Net I/σ(I): 12.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5419.60.8620.990.1980.8851.08499.7
2.54-2.5919.70.7220.9870.1650.7411.161100
2.59-2.6419.80.7020.9850.160.7211.192100
2.64-2.6919.70.560.9910.1290.5751.235100
2.69-2.7519.80.4660.9950.1080.4791.315100
2.75-2.8219.50.4190.9910.0970.431.36199.8
2.82-2.8919.60.3610.9930.0830.371.538100
2.89-2.9619.80.2720.9940.0620.2791.783100
2.96-3.0519.10.2520.9940.0590.2591.85100
3.05-3.1519.30.2030.9950.0470.2092.305100
3.15-3.2619.30.1880.9960.0440.1942.435100
3.26-3.3918.60.1570.9970.0380.1612.873100
3.39-3.5518.50.130.9980.0310.1343.472100
3.55-3.7317.70.1120.9980.0280.1163.832100
3.73-3.9717.50.1070.9980.0260.114.311100
3.97-4.2716.70.0950.9980.0240.0984.77399.8
4.27-4.716.40.0820.9990.0220.0855.02399.8
4.7-5.3815.40.0830.990.0230.0865.23399.8
5.38-6.7815.80.0820.9960.0210.0854.88198.7
6.78-5012.70.070.9960.0210.0736.7996.3

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGS

1kgs


Resolution: 2.487→38.25 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.49
RfactorNum. reflection% reflection
Rfree0.238 398 4.76 %
Rwork0.2254 --
obs0.226 8354 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 167.38 Å2 / Biso mean: 71.9301 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 2.487→38.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1876 0 0 40 1916
Biso mean---48.78 -
Num. residues----241
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021890
X-RAY DIFFRACTIONf_angle_d0.5592545
X-RAY DIFFRACTIONf_chiral_restr0.043311
X-RAY DIFFRACTIONf_plane_restr0.003326
X-RAY DIFFRACTIONf_dihedral_angle_d15.219737
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 (%)
2.4868-2.84660.30681010.28672520262196
2.8466-3.5860.30211570.261826182775100
3.586-38.25440.19721400.228182958100

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