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- PDB-1ox9: Crystal structure of SspB-ssrA complex -

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Basic information

Entry
Database: PDB / ID: 1ox9
TitleCrystal structure of SspB-ssrA complex
Components
  • Stringent starvation protein B
  • ssrA
KeywordsHYDROLASE ACTIVATOR / SspB-ssrA
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 / MOLECULAR REPLACEMENT / Resolution: 2.9 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
Revision 1.3Feb 14, 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

Downloads & links

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Assembly

Deposited unit
A: Stringent starvation protein B
I: ssrA
B: Stringent starvation protein B
J: ssrA
C: Stringent starvation protein B
K: ssrA
D: Stringent starvation protein B
L: ssrA
E: Stringent starvation protein B
M: ssrA
F: Stringent starvation protein B
N: ssrA
G: Stringent starvation protein B
O: ssrA
H: Stringent starvation protein B
P: ssrA


Theoretical massNumber of molelcules
Total (without water)103,08416
Polymers103,08416
Non-polymers00
Water00
1
A: Stringent starvation protein B
I: ssrA
B: Stringent starvation protein B
J: ssrA


Theoretical massNumber of molelcules
Total (without water)25,7714
Polymers25,7714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-13 kcal/mol
Surface area11760 Å2
MethodPISA
2
C: Stringent starvation protein B
K: ssrA
D: Stringent starvation protein B
L: ssrA


Theoretical massNumber of molelcules
Total (without water)25,7714
Polymers25,7714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-12 kcal/mol
Surface area11610 Å2
MethodPISA
3
E: Stringent starvation protein B
M: ssrA
F: Stringent starvation protein B
N: ssrA


Theoretical massNumber of molelcules
Total (without water)25,7714
Polymers25,7714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-13 kcal/mol
Surface area11720 Å2
MethodPISA
4
G: Stringent starvation protein B
O: ssrA
H: Stringent starvation protein B
P: ssrA


Theoretical massNumber of molelcules
Total (without water)25,7714
Polymers25,7714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-12 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.513, 81.524, 131.773
Angle α, β, γ (deg.)90.00, 92.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Stringent starvation protein B


Mass: 12018.668 Da / Num. of mol.: 8 / Fragment: Residues 4-111
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: Protein/peptide
ssrA


Mass: 866.830 Da / Num. of mol.: 8 / Source method: obtained synthetically
Details: This ssrA peptide is synthesized and occurs naturally in E. coli.

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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: 4.29 Å3/Da / Density % sol: 71.11 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8K, pH 8.0, 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 mMsodium cacodylate1reservoirpH6.5
7200 mMmagnesium acetate1reservoir
815-18 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 30, 2001
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 34398 / % possible obs: 93.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.9→2.99 Å / % possible all: 89.9
Reflection
*PLUS
Num. measured all: 86232 / Rmerge(I) obs: 0.124
Reflection shell
*PLUS
% possible obs: 89.9 % / Rmerge(I) obs: 0.236

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.297 3411 RANDOM
Rwork0.243 --
obs0.245 30859 -
all-34270 -
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7280 0 0 0 7280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.43
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS

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