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- PDB-1oul: Structure of the AAA+ protease delivery protein SspB -

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Basic information

Entry
Database: PDB / ID: 1oul
TitleStructure of the AAA+ protease delivery protein SspB
ComponentsStringent starvation protein B homolog
KeywordsTRANSPORT PROTEIN / ssrA peptide binding protein / homodimer
Function / homology
Function and homology information


positive regulation of protein catabolic process / ribosome / 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 homolog
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsLevchenko, I. / Grant, R.A. / Wah, D.A. / Sauer, R.T. / Baker, T.A.
Citation
Journal: Mol.Cell / Year: 2003
Title: Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag
Authors: Levchenko, I. / Grant, R.A. / Wah, D.A. / Sauer, R.T. / Baker, T.A.
#1: Journal: Science / Year: 2000
Title: A specificity-enhancing factor for the ClpXP degradation machine
Authors: Levchenko, I. / Siedel, M. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 24, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6022
Polymers29,6022
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-8 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.883, 78.883, 105.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Detailsthe biological homodimers consists of chains A and B together

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Components

#1: Protein Stringent starvation protein B homolog


Mass: 14801.002 Da / Num. of mol.: 2 / Fragment: residues 1-129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: SSPB / Production host: Escherichia coli (E. coli) / References: UniProt: P45206
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.35 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: sodium formate, sodium cacodylate, ammonium sulfate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.6 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.7 mg/mlprotein1drop
20.24 Mcalcium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH5.6
412 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97898, 0.97939, 0.96866
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2002
RadiationMonochromator: two crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978981
20.979391
30.968661
ReflectionResolution: 2.1→20 Å / Num. all: 23481 / Num. obs: 22666 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.092
Reflection shellResolution: 2.1→2.17 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.72 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 236909.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Reflection count for refinement statistics are approximately twice as large as the scaling reflection count because the refinement statistics do not reflect the merging of Bjvoet pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.292 3516 9.9 %RANDOM
Rwork0.256 ---
all0.27 42769 --
obs0.256 35659 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.283 Å2 / ksol: 0.362347 e/Å3
Displacement parametersBiso mean: 49.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.92 Å20 Å20 Å2
2---5.92 Å20 Å2
3---11.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1947 0 0 65 2012
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 602 10.8 %
Rwork0.34 4998 -
obs--90.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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