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- PDB-7lcm: Receiver Domain of RssB bound to beryllofluoride -

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Basic information

Entry
Database: PDB / ID: 7lcm
TitleReceiver Domain of RssB bound to beryllofluoride
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
BERYLLIUM TRIFLUORIDE ION / Regulator of RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDeaconescu, A.M. / Schwartz, J. / Son, 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 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6563
Polymers14,5661
Non-polymers902
Water79344
1
A: Regulator of RpoS
hetero molecules

A: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3136
Polymers29,1322
Non-polymers1814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2270 Å2
ΔGint-17 kcal/mol
Surface area12720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.329, 46.329, 95.891
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-327-

HOH

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Components

#1: Protein Regulator of RpoS


Mass: 14566.069 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MG1655 / Gene: rssB / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEV1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.8
Details: 0.2M lithium sulfate, 22% PEG 3,350, and 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-C / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→40.12 Å / Num. obs: 9736 / % possible obs: 99.5 % / Redundancy: 9.3 % / Biso Wilson estimate: 35.97 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.028 / Net I/σ(I): 21
Reflection shellResolution: 1.91→1.95 Å / Mean I/σ(I) obs: 1.7 / Num. unique obs: 908 / CC1/2: 0.69 / Rpim(I) all: 0.366

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Processing

Software
NameVersionClassification
PHENIX1.19_4080refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7L9C

7l9c


Resolution: 1.91→40.12 Å / SU ML: 0.1592 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.1339
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 968 9.95 %RANDOM
Rwork0.2022 8764 --
obs0.2065 9732 99.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.01 Å2
Refinement stepCycle: LAST / Resolution: 1.91→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms987 0 5 44 1036
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00791004
X-RAY DIFFRACTIONf_angle_d1.10381359
X-RAY DIFFRACTIONf_chiral_restr0.0642165
X-RAY DIFFRACTIONf_plane_restr0.0091173
X-RAY DIFFRACTIONf_dihedral_angle_d5.6553135
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.010.30491320.25331207X-RAY DIFFRACTION96.26
2.01-2.130.26661360.21551208X-RAY DIFFRACTION100
2.13-2.30.26521370.20451233X-RAY DIFFRACTION100
2.3-2.530.27191370.20541241X-RAY DIFFRACTION100
2.53-2.90.25711400.23311258X-RAY DIFFRACTION99.93
2.9-3.650.24641380.20571264X-RAY DIFFRACTION100
3.65-40.120.22561480.18471353X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 12.0058862267 Å / Origin y: -10.5907234563 Å / Origin z: 9.23832018953 Å
111213212223313233
T0.299500005773 Å2-0.0172693206935 Å20.0255079331211 Å2-0.251690271189 Å2-0.0269910151202 Å2--0.292501172857 Å2
L1.85281315809 °2-1.0300897804 °2-0.227881543851 °2-2.71791969133 °21.23644472554 °2--2.14386715094 °2
S-0.118283863784 Å °0.217815953706 Å °-0.260081711265 Å °-0.134125485866 Å °-0.0224704970798 Å °0.177018417387 Å °0.221222961644 Å °-0.119963460379 Å °0.124517980367 Å °
Refinement TLS groupSelection details: all

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