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- PDB-7l9c: Receiver Domain of RssB -

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Basic information

Entry
Database: PDB / ID: 7l9c
TitleReceiver Domain of RssB
ComponentsRegulator of RpoS
KeywordsSIGNALING PROTEIN / receiver domain / response regulator / ClpXP adaptor
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / positive regulation of proteolysis / protein-DNA complex / protein destabilization / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / cytosol
Similarity search - Function
Regulator of RpoS / : / PPM-type phosphatase-like domain superfamily / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDeaconescu, A.M. / Son, J. / Schwartz, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121975 United States
CitationJournal: Protein Sci. / Year: 2021
Title: Phospho-dependent signaling during the general stress response by the atypical response regulator and ClpXP adaptor RssB.
Authors: Schwartz, J. / Son, J. / Brugger, C. / Deaconescu, A.M.
History
DepositionJan 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Regulator of RpoS


Theoretical massNumber of molelcules
Total (without water)14,5661
Polymers14,5661
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.459, 46.459, 95.847
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Components on special symmetry positions
IDModelComponents
11A-221-

HOH

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Components

#1: Protein Regulator of RpoS


Mass: 14566.069 Da / Num. of mol.: 1 / Fragment: Receiver Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MG1655 / Gene: rssB / Plasmid: pSKB2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AEV1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.2M lithium sulfate, 22% PEG 3,350, 0.1M Tris-HCl pH 8.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.85→40.23 Å / Num. obs: 21241 / % possible obs: 98.91 % / Redundancy: 10.5 % / Biso Wilson estimate: 36.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.015 / Rrim(I) all: 0.051 / Rsym value: 0.05 / Net I/σ(I): 24.77
Reflection shellResolution: 1.85→1.89 Å / Num. unique obs: 977 / CC1/2: 0.8 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OD1

6od1


Resolution: 1.85→37.1 Å / SU ML: 0.1692 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.7159
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 1052 9.89 %RANDOM
Rwork0.2004 9580 --
obs0.2031 10632 98.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.85 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms976 0 0 36 1012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085997
X-RAY DIFFRACTIONf_angle_d1.11041353
X-RAY DIFFRACTIONf_chiral_restr0.0668166
X-RAY DIFFRACTIONf_plane_restr0.0105173
X-RAY DIFFRACTIONf_dihedral_angle_d5.5187136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.930.33511230.26481113X-RAY DIFFRACTION93.49
1.93-2.040.25971290.20971152X-RAY DIFFRACTION98.92
2.04-2.160.26231340.23271183X-RAY DIFFRACTION100
2.16-2.330.25621300.18311203X-RAY DIFFRACTION99.93
2.33-2.560.28291320.23421195X-RAY DIFFRACTION99.7
2.57-2.930.2371300.22541199X-RAY DIFFRACTION100
2.94-3.70.22861360.20881226X-RAY DIFFRACTION99.42
3.7-37.10.19411380.17631309X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: 10.9165202185 Å / Origin y: -10.9724718944 Å / Origin z: 9.4732087791 Å
111213212223313233
T0.317839594565 Å2-0.0177440008363 Å20.0294944433358 Å2-0.258533070041 Å2-0.00110135243084 Å2--0.288432656325 Å2
L0.892836706359 °2-0.574871668099 °2-0.294479595941 °2-2.13490711632 °21.20276590967 °2--0.747067952807 °2
S-0.112499416587 Å °0.0684954847784 Å °-0.114967806059 Å °-0.0746498377149 Å °0.0501918455155 Å °0.117897107863 Å °0.0672400727149 Å °-0.0104028142933 Å °0.00071198633047 Å °
Refinement TLS groupSelection details: all

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