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- PDB-6z4e: The structure of the C-terminal domain of RssB from E. coli -

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Basic information

Entry
Database: PDB / ID: 6z4e
TitleThe structure of the C-terminal domain of RssB from E. coli
ComponentsRegulator of RpoS
KeywordsSTRUCTURAL PROTEIN / Regulation / Stress response
Function / homology
Function and homology information


sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / phosphorelay signal transduction system / positive regulation of proteolysis / protein-DNA complex / protein destabilization / regulation of gene expression / hydrolase activity / transcription cis-regulatory region binding ...sigma factor antagonist activity / sigma factor antagonist complex / phosphorelay response regulator activity / phosphorelay signal transduction system / positive regulation of proteolysis / protein-DNA complex / protein destabilization / regulation of gene expression / hydrolase activity / 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
Regulator of RpoS / Regulator of RpoS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsZeth, K. / Dimce, M. / Terrence, D.M. / Schuenemann, V. / Dougan, D.
CitationJournal: Biomolecules / Year: 2020
Title: Insight into the RssB-Mediated Recognition and Delivery of sigma s to the AAA+ Protease, ClpXP.
Authors: Micevski, D. / Zeth, K. / Mulhern, T.D. / Schuenemann, V.J. / Zammit, J.E. / Truscott, K.N. / Dougan, D.A.
History
DepositionMay 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)37,3381
Polymers37,3381
Non-polymers00
Water2,594144
1
A: Regulator of RpoS

A: Regulator of RpoS


Theoretical massNumber of molelcules
Total (without water)74,6762
Polymers74,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area1460 Å2
ΔGint-4 kcal/mol
Surface area18500 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.239, 56.239, 294.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: C3TCP2, UniProt: P0AEV1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.93 Å3/Da / Density % sol: 57.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 20% PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18222 / % possible obs: 91.8 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.2
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 1408 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 2→37.533 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 912 5 %RANDOM
Rwork0.2118 ---
obs0.2133 18222 91.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→37.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 0 144 1759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031686
X-RAY DIFFRACTIONf_angle_d0.632299
X-RAY DIFFRACTIONf_dihedral_angle_d2.3651400
X-RAY DIFFRACTIONf_chiral_restr0.042261
X-RAY DIFFRACTIONf_plane_restr0.003307
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.35331360.30722575X-RAY DIFFRACTION99
2.1055-2.23740.37741200.26852274X-RAY DIFFRACTION89
2.2374-2.41020.3106890.22871699X-RAY DIFFRACTION99
2.4102-2.65270.27391390.22292649X-RAY DIFFRACTION100
2.6527-3.03640.25181410.22612679X-RAY DIFFRACTION100
3.0364-3.82490.22111310.20352490X-RAY DIFFRACTION91
3.8249-37.530.20471560.18652944X-RAY DIFFRACTION100
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)
12.8621.6593-2.09035.6423-2.9213.50750.3318-0.59080.15932.0418-0.1129-0.3592-0.80980.0347-0.00740.379-0.0778-0.09770.7134-0.03010.386413.483720.117958.3486
22.48220.01110.18663.1195-0.27362.08790.003-0.5119-0.04560.57740.0390.2382-0.13230.1168-0.03480.2995-0.08410.02460.5970.00180.30211.651918.636757.6129
30.58850.3730.69434.4129-0.60362.51960.0333-0.0012-0.08250.52560.13870.3454-0.1972-0.1194-0.2410.2608-0.06590.05160.4236-0.04570.32257.009934.823246.9593
42.0061-0.4016-1.06072.1014-0.65331.91530.09130.00690.37590.05740.01040.12690.00310.0421-0.11120.207-0.07450.01970.4195-0.0040.28068.676324.995842.8863
53.31820.4577-0.64282.5539-0.42954.4719-0.137-0.0539-0.3563-0.17030.0746-0.33130.62940.36030.0920.2541-0.01590.02850.3533-0.00510.277913.783915.764241.3695
62.09030.1734-0.45223.4076-1.15362.7696-0.3247-0.0312-0.3426-0.42140.2463-0.18840.4152-0.1033-0.09010.2637-0.0620.03410.327-0.03390.25777.177119.389839.8523
71.63760.99761.3392.8718-0.28521.5711-0.0951-0.1939-0.2616-0.460.1395-0.52940.08180.4699-0.05080.3031-0.13360.08520.4674-0.08570.336817.122329.37233.0154
83.38711.1127-1.26834.1344-1.60123.7176-0.1810.00470.5203-0.46980.2341-0.1458-0.05420.24210.2230.4199-0.12850.01090.4278-0.03410.34754.506632.844528.5864
91.41091.458-1.45071.6943-1.73751.7565-0.89950.9794-0.1523-1.55670.9060.2251.3434-0.72420.17680.7452-0.28230.04680.5085-0.06770.41263.893814.709531.5222
101.0137-0.35190.36933.16710.18891.7367-0.08850.37030.3039-0.48180.14420.0504-0.24180.05650.13340.2939-0.15420.00590.3508-0.03250.2918.715734.490735.4283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 102 through 112 )
2X-RAY DIFFRACTION2chain 'A' and (resid 113 through 131 )
3X-RAY DIFFRACTION3chain 'A' and (resid 132 through 156 )
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 180 )
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 225 )
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 240 )
7X-RAY DIFFRACTION7chain 'A' and (resid 241 through 251 )
8X-RAY DIFFRACTION8chain 'A' and (resid 252 through 267 )
9X-RAY DIFFRACTION9chain 'A' and (resid 268 through 282 )
10X-RAY DIFFRACTION10chain 'A' and (resid 283 through 308 )

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