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- PDB-1ox8: Crystal structure of SspB -

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Basic information

Entry
Database: PDB / ID: 1ox8
TitleCrystal structure of SspB
ComponentsStringent starvation protein B
KeywordsHYDROLASE ACTIVATOR / RNA-binding property
Function / homology
Function and homology information


positive regulation of proteolysis involved in protein catabolic process / HslUV protease complex / positive regulation of ATP-dependent activity / positive regulation of protein catabolic process / ATPase binding / molecular adaptor activity / ribosome / protein homodimerization activity / RNA binding / cytosol
Similarity search - Function
SspB-like / Stringent starvation protein B / SspB-like superfamily / Stringent starvation protein B / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Stringent starvation protein B / Stringent starvation protein B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsSong, H.K. / Eck, M.J.
CitationJournal: Mol.Cell / Year: 2003
Title: Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine
Authors: Song, H.K. / Eck, M.J.
History
DepositionApr 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Stringent starvation protein B
B: Stringent starvation protein B


Theoretical massNumber of molelcules
Total (without water)24,0512
Polymers24,0512
Non-polymers00
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.116, 60.116, 187.984
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Stringent starvation protein B


Mass: 12025.380 Da / Num. of mol.: 2 / Fragment: Residues 5-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: O157:H7 / Gene: SSPB OR B3228 OR Z4586 OR ECS4101 / Production host: Escherichia coli (E. coli) / References: UniProt: P25663, UniProt: P0AFZ3*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: 3.29 Å3/Da / Density % sol: 62.38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
250 mMTris-HCl1droppH7.7
3250 mM1dropNaCl
42 mMEDTA1drop
52 mMbeta-mercaptoethanol1drop
6100 mMHEPES-KOH1reservoirpH7.5
74.0-4.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 1, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 18454 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.2→2.26 Å / % possible all: 100
Reflection
*PLUS
% possible obs: 100 % / Num. measured all: 503846 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.196

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
DMmodel building
CNSrefinement
HKL-2000data reduction
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1649 -RANDOM
Rwork0.248 ---
obs0.249 15100 9 %-
all-16749 --
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 0 144 1830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.38
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS

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