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- PDB-8svz: Structure of the Francisella response regulator KdpE receiver domain -

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Basic information

Entry
Database: PDB / ID: 8svz
TitleStructure of the Francisella response regulator KdpE receiver domain
ComponentsTwo-component response regulator
KeywordsTRANSCRIPTION / response regulator / transcription regulator / two-component system
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / Two-component response regulator
Similarity search - Component
Biological speciesFrancisella tularensis subsp. novicida U112 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsMilton, M.E. / Cavanagh, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Insights into DNA-binding motifs and mechanisms of Francisella tularensis novicida two-component system response regulator proteins QseB, KdpE, and BfpR.
Authors: Gaddy, K.E. / Bensch, E.M. / Cavanagh, J. / Milton, M.E.
History
DepositionMay 17, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Two-component response regulator
B: Two-component response regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1966
Polymers29,0152
Non-polymers1814
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-21 kcal/mol
Surface area12040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.708, 134.708, 123.118
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 119)
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: 1 - 119 / Label seq-ID: 4 - 122

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.757745159909, -0.45641966837, -0.466372553823), (0.473492326676, 0.107222445667, -0.874247312678), (0.449029274338, -0.883280495353, 0.13486392148)Vector: 55. ...NCS oper: (Code: given
Matrix: (-0.757745159909, -0.45641966837, -0.466372553823), (0.473492326676, 0.107222445667, -0.874247312678), (0.449029274338, -0.883280495353, 0.13486392148)
Vector: 55.8032024248, -18.2063637538, -27.6766665519)

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Components

#1: Protein Two-component response regulator


Mass: 14507.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. novicida U112 (bacteria)
Strain: U112 / Gene: kdpE, FTN_1714, AW25_274 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0Q8K6
#2: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 6 Å3/Da / Density % sol: 79.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5 M ammonium sulfate, 0.1 M Tris pH 8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.34→50 Å / Num. obs: 10007 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 168.95 Å2 / CC1/2: 0.961 / CC star: 0.99 / Rpim(I) all: 0.057 / Rrim(I) all: 0.193 / Rsym value: 0.184 / Net I/σ(I): 24.825
Reflection shellResolution: 3.34→3.4 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 0.326 / Num. unique obs: 487 / CC1/2: 0.12 / CC star: 0.463 / Rpim(I) all: 2.345 / Rrim(I) all: 7.345 / Rsym value: 6.945 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000720data reduction
HKL-2000720data scaling
PHASER1.20.1_4487phasing
JBluIce-EPICSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→45.44 Å / SU ML: 0.6225 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.3127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2487 991 10 %
Rwork0.2279 8916 -
obs0.2301 9907 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 180.51 Å2
Refinement stepCycle: LAST / Resolution: 3.35→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1888 0 10 14 1912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00281922
X-RAY DIFFRACTIONf_angle_d0.61472603
X-RAY DIFFRACTIONf_chiral_restr0.0483308
X-RAY DIFFRACTIONf_plane_restr0.0152335
X-RAY DIFFRACTIONf_dihedral_angle_d5.2472253
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.939870704182 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.520.46121330.44181191X-RAY DIFFRACTION94.71
3.52-3.740.38421380.31321245X-RAY DIFFRACTION99.78
3.74-4.030.28991380.29941239X-RAY DIFFRACTION99.64
4.03-4.440.27321400.2221269X-RAY DIFFRACTION99.93
4.44-5.080.23151430.20081280X-RAY DIFFRACTION99.86
5.08-6.40.28311450.27071299X-RAY DIFFRACTION99.93
6.4-45.440.21431540.19551393X-RAY DIFFRACTION99.74
Refinement TLS params.Method: refined / Origin x: 39.5120834089 Å / Origin y: -28.0292273425 Å / Origin z: 21.390693447 Å
111213212223313233
T1.28279602613 Å2-0.0788727610586 Å2-0.101074112826 Å2-1.09938433536 Å20.161335332527 Å2--1.0035913853 Å2
L2.76196954429 °2-0.287212470021 °2-0.158399916548 °2-5.16962711906 °22.4797529558 °2--2.89229716818 °2
S-0.0833556921285 Å °0.0853072061207 Å °0.42362245025 Å °-0.712602887125 Å °0.0103290682815 Å °-0.217507863729 Å °-0.561200295546 Å °-0.0214133907597 Å °0.070583302357 Å °
Refinement TLS groupSelection details: all

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