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- PDB-3eod: Crystal structure of N-terminal domain of E. coli RssB -

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Basic information

Entry
Database: PDB / ID: 3eod
TitleCrystal structure of N-terminal domain of E. coli RssB
ComponentsProtein hnr
KeywordsSIGNALING PROTEIN / response regulator / Phosphoprotein / Two-component regulatory system
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 / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsLevchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: To be Published
Title: The structure of RssB, a ClpX adaptor protein that regulates sigma S
Authors: Levchenko, I. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 21, 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: Protein hnr


Theoretical massNumber of molelcules
Total (without water)14,3881
Polymers14,3881
Non-polymers00
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.114, 45.114, 96.797
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

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Components

#1: Protein Protein hnr


Mass: 14387.857 Da / Num. of mol.: 1 / Fragment: Response regulatory domain, UNP residues 1-130
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: b1235, hnr, JW1223, rssb, ychL / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEV1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.75
Details: 0.1 M Tris-HCl, 0.2 Na Acetate, 1 mM DTT, 28% PEG3350, 1.9 mg/ml protein, pH 8.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97932,1.0070,1.0087
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 5, 2005
RadiationMonochromator: crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
21.0071
31.00871
ReflectionRedundancy: 9.5 % / Av σ(I) over netI: 80.73 / Number: 88255 / Rmerge(I) obs: 0.072 / Χ2: 1.26 / D res high: 2.35 Å / D res low: 50 Å / Num. obs: 9277 / % possible obs: 99.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.065096.510.0562.2919.4
4.025.0698.810.0632.2889.8
3.514.0299.810.0732.03710.2
3.193.5110010.0731.49110.1
2.963.1910010.0881.15210
2.792.9610010.1180.8099.9
2.652.7910010.1570.6949.8
2.532.6599.910.2020.5849.5
2.432.5399.510.2560.4768.9
2.352.4397.410.3230.4767.6
ReflectionResolution: 1.75→50 Å / Num. obs: 12003 / % possible obs: 99.1 % / Redundancy: 38.6 % / Rmerge(I) obs: 0.061 / Χ2: 1.3 / Net I/σ(I): 80.733
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.75-1.8123.50.46411460.4498
1.81-1.8937.20.35611730.49199.7
1.89-1.9742.20.24711920.64199.7
1.97-2.0742.80.16811780.78499.7
2.07-2.242.90.12211910.99199.9
2.2-2.3842.70.09412081.285100
2.38-2.6142.40.07712001.492100
2.61-2.9941.90.07112211.966100
2.99-3.7739.10.05912342.52799.9
3.77-5031.30.04412602.09194.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MAD / Resolution: 1.75→39.07 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.825 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 0.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1221 10.3 %random
Rwork0.224 ---
all0.999 ---
obs0.227 11854 98.2 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.362 e/Å3
Displacement parametersBiso max: 119.35 Å2 / Biso mean: 58.925 Å2 / Biso min: 29.27 Å2
Baniso -1Baniso -2Baniso -3
1--5.386 Å2-0 Å2-0 Å2
2---5.386 Å20 Å2
3----15.913 Å2
Refinement stepCycle: LAST / Resolution: 1.75→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms941 0 0 52 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004961
X-RAY DIFFRACTIONf_angle_d0.8391315
X-RAY DIFFRACTIONf_chiral_restr0.05162
X-RAY DIFFRACTIONf_plane_restr0.004169
X-RAY DIFFRACTIONf_dihedral_angle_d13.33380
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.820.2881210.2461095121694
1.82-1.9020.2711380.2311150128897
1.902-2.0030.2871360.2171149128599
2.003-2.1280.2251340.2111180131499
2.128-2.2920.261340.20411901324100
2.292-2.5230.2641090.21612261335100
2.523-2.8880.2591430.23411921335100
2.888-3.6380.2441420.21312241366100
3.638-39.080.261640.2281227139195

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