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- PDB-3o2o: Structure of E. coli ClpS ring complex -

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Basic information

Entry
Database: PDB / ID: 3o2o
TitleStructure of E. coli ClpS ring complex
ComponentsATP-dependent Clp protease adaptor protein ClpS
KeywordsPEPTIDE BINDING PROTEIN / adaptor / N-end rule peptide / peptide-binding protein
Function / homology
Function and homology information


molecular function inhibitor activity / protein catabolic process / response to heat / protein-folding chaperone binding / proteolysis
Similarity search - Function
Ribosomal protein L7/L12, C-terminal domain/Adaptor protein ClpS / ATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsRoman-Hernandez, G. / Grant, R.A. / Sauer, R.T. / Baker, T.A. / de Regt, A.
CitationJournal: Embo Rep. / Year: 2009
Title: Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS.
Authors: Schuenemann, V.J. / Kralik, S.M. / Albrecht, R. / Spall, S.K. / Truscott, K.N. / Dougan, D.A. / Zeth, K.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 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
Remark 0THIS ENTRY 3O2O REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2WA9 ORIGINAL DATA ...THIS ENTRY 3O2O REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2WA9 ORIGINAL DATA DETERMINED BY AUTHOR: V.J.SCHUENEMANN,S.M.KRALIK,R.ALBRECHT,S.K.SPALL,K.N.TRUSCOTT,D.A.DOUGAN,K.ZETH

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent Clp protease adaptor protein ClpS
B: ATP-dependent Clp protease adaptor protein ClpS
C: ATP-dependent Clp protease adaptor protein ClpS
D: ATP-dependent Clp protease adaptor protein ClpS
E: ATP-dependent Clp protease adaptor protein ClpS
F: ATP-dependent Clp protease adaptor protein ClpS
G: ATP-dependent Clp protease adaptor protein ClpS
H: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)77,8118
Polymers77,8118
Non-polymers00
Water0
1
A: ATP-dependent Clp protease adaptor protein ClpS
B: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent Clp protease adaptor protein ClpS
C: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent Clp protease adaptor protein ClpS
D: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ATP-dependent Clp protease adaptor protein ClpS
E: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ATP-dependent Clp protease adaptor protein ClpS
F: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ATP-dependent Clp protease adaptor protein ClpS
G: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ATP-dependent Clp protease adaptor protein ClpS
H: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
A: ATP-dependent Clp protease adaptor protein ClpS
H: ATP-dependent Clp protease adaptor protein ClpS


Theoretical massNumber of molelcules
Total (without water)19,4532
Polymers19,4532
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.910, 155.870, 71.230
Angle α, β, γ (deg.)90.000, 114.640, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ATP-dependent Clp protease adaptor protein ClpS /


Mass: 9726.334 Da / Num. of mol.: 8 / Fragment: unp residues 22-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clpS / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q6

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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: 5.57 Å3/Da / Density % sol: 77.93 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium Nitrate 20% PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twinOperator: k+l,h+l,-l / Fraction: 0.411
ReflectionResolution: 2.9→25 Å / Num. obs: 37634 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→24.967 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7291 / σ(F): 1.99 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 1883 5 %random
Rwork0.1734 ---
obs0.1754 37634 99.9 %-
all-37634 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.163 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 171.38 Å2 / Biso mean: 80.345 Å2 / Biso min: 29.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.99 Å20 Å22.4079 Å2
2---1.2129 Å2-0 Å2
3----2.7771 Å2
Refinement stepCycle: LAST / Resolution: 2.9→24.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5380 0 0 0 5380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055499
X-RAY DIFFRACTIONf_angle_d0.7887470
X-RAY DIFFRACTIONf_chiral_restr0.04873
X-RAY DIFFRACTIONf_plane_restr0.004945
X-RAY DIFFRACTIONf_dihedral_angle_d12.6372018
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 95 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9005-2.97870.32271430.293427102853
2.9787-3.06620.29921440.277427392883
3.0662-3.16490.32891430.251427122855
3.1649-3.27770.28741450.24927502895
3.2777-3.40860.26291470.227328002947
3.4086-3.56320.24111430.209227162859
3.5632-3.75030.22231450.190127552900
3.7503-3.98420.19441430.16927222865
3.9842-4.290.18061460.150327582904
4.29-4.71840.14871430.136127252868
4.7184-5.39370.16121450.147327662911
5.3937-6.76740.17591460.158327652911
6.7674-23.19680.15081480.129728022950

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