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- PDB-3o2h: E. coli ClpS in complex with a Leu N-end rule peptide -

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Basic information

Entry
Database: PDB / ID: 3o2h
TitleE. coli ClpS in complex with a Leu N-end rule peptide
Components
  • ATP-dependent Clp protease adaptor protein ClpS
  • DNA protection during starvation protein
KeywordsPEPTIDE BINDING PROTEIN / adaptor / protein-peptide complex / peptide-binding protein / N-end rule peptide
Function / homology
Function and homology information


DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / molecular function inhibitor activity / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / protein catabolic process ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / molecular function inhibitor activity / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding / protein catabolic process / protein-folding chaperone binding / response to heat / intracellular iron ion homeostasis / proteolysis / DNA binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
DNA protection during starvation protein, gammaproteobacteria / 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 / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ribosomal Protein L30; Chain: A, ...DNA protection during starvation protein, gammaproteobacteria / 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 / Dps protein family signature 2. / Dps protein family signature 1. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ribosomal Protein L30; Chain: A, / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-dependent Clp protease adapter protein ClpS / DNA protection during starvation protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 3O2H REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2W9R ORIGINAL DATA ...THIS ENTRY 3O2H REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2W9R 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: DNA protection during starvation protein


Theoretical massNumber of molelcules
Total (without water)13,3132
Polymers13,3132
Non-polymers00
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-5 kcal/mol
Surface area7490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.080, 28.230, 38.910
Angle α, β, γ (deg.)97.44, 106.45, 92.39
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 12061.842 Da / Num. of mol.: 1
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
#2: Protein/peptide DNA protection during starvation protein / PEXB / VTM


Mass: 1251.515 Da / Num. of mol.: 1 / Fragment: unp residues 6-16 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
References: UniProt: P0ABT2, Oxidoreductases; Oxidizing metal ions
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.41 Å3/Da / Density % sol: 43.98 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Sodium Acetate, 0.1 M TRIS, 30% PEG 4000, pH 8.5, 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
RadiationMonochromator: beamline / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 1 / Num. obs: 12445 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→18.455 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.55 / σ(F): 1.95 / Phase error: 25.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2242 574 4.99 %
Rwork0.1989 --
obs0.2002 11494 92.4 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.657 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7766 Å20.1059 Å20.118 Å2
2--0.8579 Å2-2.4603 Å2
3---0.8947 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms843 0 0 121 964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009862
X-RAY DIFFRACTIONf_angle_d1.1681169
X-RAY DIFFRACTIONf_dihedral_angle_d13.609323
X-RAY DIFFRACTIONf_chiral_restr0.062139
X-RAY DIFFRACTIONf_plane_restr0.005147
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.87120.33361460.28012781X-RAY DIFFRACTION93
1.8712-2.14160.28521440.2132736X-RAY DIFFRACTION93
2.1416-2.69680.22491440.19532731X-RAY DIFFRACTION93
2.6968-18.45580.18811400.18292672X-RAY DIFFRACTION91

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