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- PDB-3o2b: E. coli ClpS in complex with a Phe N-end rule peptide -

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Basic information

Entry
Database: PDB / ID: 3o2b
TitleE. coli ClpS in complex with a Phe N-end rule peptide
Components
  • ATP-dependent Clp protease adaptor protein ClpS
  • Phe N-end rule peptide
KeywordsPEPTIDE BINDING PROTEIN / adaptor / protein-peptide complex / peptide-binding protein / N-end rule peptide
Function / homology
Function and homology information


molecular function inhibitor activity / protein catabolic process / protein-folding chaperone binding / response to heat / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 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 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 0THIS ENTRY 3O2B REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2WA8 ORIGINAL DATA ...THIS ENTRY 3O2B REFLECTS AN ALTERNATIVE MODELING OF THE STRUCTURAL DATA IN 2WA8 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

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Assembly

Deposited unit
A: ATP-dependent Clp protease adaptor protein ClpS
B: Phe N-end rule peptide
C: ATP-dependent Clp protease adaptor protein ClpS
D: Phe N-end rule peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6866
Polymers26,5544
Non-polymers1322
Water2,432135
1
A: ATP-dependent Clp protease adaptor protein ClpS
B: Phe N-end rule peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4094
Polymers13,2772
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-24 kcal/mol
Surface area5700 Å2
MethodPISA
2
C: ATP-dependent Clp protease adaptor protein ClpS
D: Phe N-end rule peptide


Theoretical massNumber of molelcules
Total (without water)13,2772
Polymers13,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-6 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.223, 58.405, 56.413
Angle α, β, γ (deg.)90.00, 101.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12061.842 Da / Num. of mol.: 2 / Fragment: unp residues 2-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: clpS, yljA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8Q6
#2: Protein/peptide Phe N-end rule peptide


Mass: 1215.355 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 1.96 Å3/Da / Density % sol: 37.12 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 M Lithium Sulfate, 0.1 M TRIS, 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→30.2 Å / Num. obs: 13973 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
REFMACrefinement
PDB_EXTRACT3.1data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→30.2 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.49 / σ(F): 1.92 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 862 7.01 %
Rwork0.21 --
obs0.2126 12294 94.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.968 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.6032 Å20 Å21.845 Å2
2--6.448 Å2-0 Å2
3----4.4418 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1611 0 6 135 1752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061653
X-RAY DIFFRACTIONf_angle_d1.0072239
X-RAY DIFFRACTIONf_dihedral_angle_d14.855602
X-RAY DIFFRACTIONf_chiral_restr0.06253
X-RAY DIFFRACTIONf_plane_restr0.006286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.17850.31821450.2751920X-RAY DIFFRACTION96
2.1785-2.34670.28771430.24591908X-RAY DIFFRACTION96
2.3467-2.58270.26641450.21941915X-RAY DIFFRACTION96
2.5827-2.95620.24431450.21861922X-RAY DIFFRACTION95
2.9562-3.72340.25061420.16971896X-RAY DIFFRACTION95
3.7234-30.19270.20691420.19961871X-RAY DIFFRACTION91

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