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- PDB-9by5: Crystal Structure of RT-PhyR (ruthe_01174) -

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Basic information

Entry
Database: PDB / ID: 9by5
TitleCrystal Structure of RT-PhyR (ruthe_01174)
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / Response Regulator / PhyR / anti-anti sigma factor / sigma-like / receiver
Function / homology
Function and homology information


phosphorelay signal transduction system
Similarity search - Function
Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / : / RNA polymerase sigma factor, region 3/4-like / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain ...Signal transduction response regulator PhyR-like, alphaproteobacteria / : / : / Sigma2 domain of PhyR / Response regulator PhyR, sigma-like domain / : / RNA polymerase sigma factor, region 3/4-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
Response regulator receiver protein
Similarity search - Component
Biological speciesRubellimicrobium thermophilum DSM 16684 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSwingle, D. / Isiorho, E.A. / Gardner, K.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM106239 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Variations in kinase and effector signaling logic in a bacterial two component signaling network.
Authors: Swingle, D. / Epstein, L. / Aymon, R. / Isiorho, E.A. / Abzalimov, R.R. / Favaro, D.C. / Gardner, K.H.
History
DepositionMay 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Response regulator receiver protein
B: Response regulator receiver protein
C: Response regulator receiver protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,77011
Polymers88,4833
Non-polymers2878
Water3,747208
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.910, 118.642, 121.088
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21C-422-

HOH

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Components

#1: Protein Response regulator receiver protein


Mass: 29494.291 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubellimicrobium thermophilum DSM 16684 (bacteria)
Strain: DSM 16684 / Gene: ruthe_01174 / Production host: Escherichia coli (E. coli) / References: UniProt: S9SJ09
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.24 Å3/Da / Density % sol: 46.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris.HCl pH 8.5, 16% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→34 Å / Num. obs: 56844 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 43.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.03 / Rrim(I) all: 0.112 / Net I/σ(I): 13.4
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 14.2 % / Rmerge(I) obs: 3.462 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 2789 / CC1/2: 0.352 / Rpim(I) all: 0.944 / Rrim(I) all: 3.59 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
Coot0.9.8model building
BALBESphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→34 Å / SU ML: 0.2842 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 2675 4.71 %
Rwork0.2087 54143 -
obs0.2101 56818 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.23 Å2
Refinement stepCycle: LAST / Resolution: 1.99→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5752 0 15 208 5975
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01025845
X-RAY DIFFRACTIONf_angle_d1.34417942
X-RAY DIFFRACTIONf_chiral_restr0.0656950
X-RAY DIFFRACTIONf_plane_restr0.04731041
X-RAY DIFFRACTIONf_dihedral_angle_d16.56122166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.36361340.36682794X-RAY DIFFRACTION99.42
2.02-2.060.35321230.3212825X-RAY DIFFRACTION99.9
2.06-2.10.37931390.29872818X-RAY DIFFRACTION99.9
2.1-2.150.30041110.27582845X-RAY DIFFRACTION100
2.15-2.20.311180.26232852X-RAY DIFFRACTION100
2.2-2.250.2831390.25252832X-RAY DIFFRACTION100
2.25-2.310.29791400.2552827X-RAY DIFFRACTION100
2.31-2.380.30591290.24992858X-RAY DIFFRACTION100
2.38-2.460.31141310.23822816X-RAY DIFFRACTION100
2.46-2.550.29421420.23842847X-RAY DIFFRACTION100
2.55-2.650.28111850.22562792X-RAY DIFFRACTION100
2.65-2.770.29661280.23092871X-RAY DIFFRACTION100
2.77-2.910.25881400.24012831X-RAY DIFFRACTION99.97
2.91-3.10.29311400.23982855X-RAY DIFFRACTION100
3.1-3.340.25871150.21332879X-RAY DIFFRACTION100
3.34-3.670.23431830.19572831X-RAY DIFFRACTION100
3.67-4.20.18051350.16672883X-RAY DIFFRACTION100
4.2-5.290.17981660.15772891X-RAY DIFFRACTION100
5.29-340.21481770.19972996X-RAY DIFFRACTION99.87

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