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- PDB-9cb6: Crystal Structure of RT-PhyR (ruthe_02744) -

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Basic information

Entry
Database: PDB / ID: 9cb6
TitleCrystal Structure of RT-PhyR (ruthe_02744)
ComponentsResponse regulator receiver protein
KeywordsSIGNALING PROTEIN / PhyR / histidine kinase / response regulator / general stress response / anti anti sigma factor / alphaproteobacteria / 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
Similarity search - Domain/homology
Response regulator receiver protein
Similarity search - Component
Biological speciesRubellimicrobium thermophilum DSM 16684 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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
DepositionJun 18, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 4, 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
D: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)118,3514
Polymers118,3514
Non-polymers00
Water81145
1
A: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)29,5881
Polymers29,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)29,5881
Polymers29,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)29,5881
Polymers29,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Response regulator receiver protein


Theoretical massNumber of molelcules
Total (without water)29,5881
Polymers29,5881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.101, 149.543, 73.564
Angle α, β, γ (deg.)90.000, 101.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Response regulator receiver protein


Mass: 29587.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rubellimicrobium thermophilum DSM 16684 (bacteria)
Strain: DSM 16684 / Gene: ruthe_02744 / Production host: Escherichia coli (E. coli) / References: UniProt: S9QU65
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M Bis-tris propane, 0.2M KSCN, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 5, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.83→33.85 Å / Num. obs: 30415 / % possible obs: 99.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 57.1 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.225 / Rpim(I) all: 0.135 / Rrim(I) all: 0.263 / Net I/σ(I): 2.7
Reflection shellResolution: 2.83→2.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.417 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 1502 / CC1/2: 0.361 / Rpim(I) all: 0.91 / Rrim(I) all: 1.689 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.20.1_4487refinement
autoPROCdata processing
Aimlessdata scaling
PHASERphasing
Coot0.9.8model building
BALBESphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→33.85 Å / SU ML: 0.4368 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.1848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2719 1393 4.6 %
Rwork0.2331 28912 -
obs0.2348 30305 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.09 Å2
Refinement stepCycle: LAST / Resolution: 2.83→33.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7458 0 0 45 7503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00297577
X-RAY DIFFRACTIONf_angle_d0.637410268
X-RAY DIFFRACTIONf_chiral_restr0.03921191
X-RAY DIFFRACTIONf_plane_restr0.00721365
X-RAY DIFFRACTIONf_dihedral_angle_d15.90762846
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.930.34291490.32772758X-RAY DIFFRACTION96.61
2.93-3.040.3351340.31852912X-RAY DIFFRACTION99.58
3.04-3.180.34091290.30322894X-RAY DIFFRACTION99.74
3.18-3.350.33221400.2752904X-RAY DIFFRACTION99.71
3.35-3.560.3071300.26962911X-RAY DIFFRACTION99.74
3.56-3.830.34741490.28812864X-RAY DIFFRACTION99.64
3.83-4.220.25161500.19762872X-RAY DIFFRACTION99.74
4.22-4.830.22291330.18932914X-RAY DIFFRACTION99.74
4.83-6.080.23591410.2072943X-RAY DIFFRACTION99.97
6.08-33.850.20691380.18262940X-RAY DIFFRACTION99.48

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