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- PDB-8t85: Structure of RssB bound to beryllofluoride -

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Basic information

Entry
Database: PDB / ID: 8t85
TitleStructure of RssB bound to beryllofluoride
ComponentsRegulator of RpoS
KeywordsSIGNALING PROTEIN / receiver domain / pseudophosphatase / response regulator
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 / DI(HYDROXYETHYL)ETHER / Regulator of RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsBrugger, C. / Schwartz, J. / Deaconescu, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1GM121975 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM144124 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structure of phosphorylated-like RssB, the adaptor delivering sigma s to the ClpXP proteolytic machinery, reveals an interface switch for activation.
Authors: Brugger, C. / Schwartz, J. / Novick, S. / Tong, S. / Hoskins, J.R. / Majdalani, N. / Kim, R. / Filipovski, M. / Wickner, S. / Gottesman, S. / Griffin, P.R. / Deaconescu, A.M.
History
DepositionJun 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 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: Regulator of RpoS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7476
Polymers37,3381
Non-polymers4095
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.366, 119.035, 135.973
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Regulator of RpoS


Mass: 37338.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rssB, hnr, sprE, ychL, b1235, JW1223 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEV1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 300mM magnesium nitrate hexahydrate, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-E / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.38→135.97 Å / Num. obs: 13903 / % possible obs: 99.7 % / Redundancy: 7.6 % / Biso Wilson estimate: 42.54 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.113 / Net I/σ(I): 1.1
Reflection shellResolution: 2.38→2.47 Å / Num. unique obs: 1314 / CC1/2: 0.339 / Rpim(I) all: 0.691

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OD1

6od1


Resolution: 2.38→67.99 Å / SU ML: 0.3404 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2777 1388 10.01 %
Rwork0.222 12479 -
obs0.2278 13867 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.2 Å2
Refinement stepCycle: LAST / Resolution: 2.38→67.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 26 50 2680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092668
X-RAY DIFFRACTIONf_angle_d1.08073613
X-RAY DIFFRACTIONf_chiral_restr0.0528419
X-RAY DIFFRACTIONf_plane_restr0.0165472
X-RAY DIFFRACTIONf_dihedral_angle_d8.5439370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.470.35591310.31831183X-RAY DIFFRACTION97.05
2.47-2.560.3251370.30361219X-RAY DIFFRACTION99.34
2.56-2.680.32281370.26571233X-RAY DIFFRACTION100
2.68-2.820.37541370.26441230X-RAY DIFFRACTION100
2.82-30.29781380.25521257X-RAY DIFFRACTION99.93
3-3.230.28791380.24021232X-RAY DIFFRACTION99.93
3.23-3.560.26251390.20581252X-RAY DIFFRACTION100
3.56-4.070.2911390.19251250X-RAY DIFFRACTION100
4.07-5.130.20361410.18381277X-RAY DIFFRACTION99.86
5.13-67.990.28471510.21521346X-RAY DIFFRACTION99.87
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.11076283495-0.9605784874260.7366694329715.23814919444-1.507735095332.07224475003-0.0571749388495-0.394515441127-0.07779673262860.5076838510820.1318657928020.106423654566-0.01402716598760.0447321255782-0.02983374448340.3439376056650.03453265889360.00563660943720.321674540819-0.006057181298360.277018235085-11.3689863936-47.949481253215.6576373055
21.038747217260.192464002546-0.05766095574272.876970849510.3792142035481.96303043058-0.00684036427848-0.06710224652080.06845898626870.136465374667-0.0070507489309-0.0178262860162-0.1187007639420.06887761926020.04507347903880.2510799011050.01636373801550.01165378628680.2592961971650.02058727417430.278549102887-19.969486146-20.423979698514.503536612
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 141 )3 - 1411 - 139
22chain 'A' and (resid 142 through 337 )142 - 337140 - 335

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