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- PDB-2w9r: Structural basis of N-end rule substrate recognition in Escherich... -

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Basic information

Entry
Database: PDB / ID: 2w9r
TitleStructural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS
Components
  • ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
  • DNA PROTECTION DURING STARVATION PROTEIN
KeywordsCHAPERONE / ADAPTOR PROTEIN / DNA CONDENSATION / IRON / CLPS / CLPA / CYTOPLASM / N-END RULE / DNA-BINDING / IRON STORAGE / METAL-BINDING / OXIDOREDUCTASE
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 stress / response to starvation / negative regulation of DNA-templated DNA replication initiation / ferric iron binding ...DnaA-Dps complex / Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / nucleoid / chromosome condensation / molecular function inhibitor activity / response to stress / 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 / OTHER / Resolution: 1.7 Å
AuthorsSchuenemann, V. / Kralik, S.M. / Albrecht, R. / Spall, S.K. / Truscott, K.N. / Dougan, D.A. / Zeth, K.
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
DepositionJan 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
B: DNA PROTECTION DURING STARVATION PROTEIN


Theoretical massNumber of molelcules
Total (without water)13,5732
Polymers13,5732
Non-polymers00
Water1,22568
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-5.04 kcal/mol
Surface area7700 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 ADAPTER PROTEIN CLPS / YLJA


Mass: 12321.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLPS PROTEIN FROM ESCHERICHIA COLI IN COMPLEX WITH LEU-PEPTIDE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A8Q6
#2: Protein/peptide DNA PROTECTION DURING STARVATION PROTEIN / PEXB / VTM


Mass: 1251.515 Da / Num. of mol.: 1 / Fragment: RESIDUES 10-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0ABT2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.3 Å3/Da / Density % sol: 48 % / Description: NONE
Crystal growpH: 7 / Details: pH 7

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationProtocol: 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. obs: 11540 / % possible obs: 91.1 % / Observed criterion σ(I): 4 / Redundancy: 2.1 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.186 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 574 5 %RANDOM
Rwork0.226 ---
obs0.228 10925 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.38 Å21.15 Å2
2---0.66 Å2-0.33 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms856 0 0 68 924
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1931.9851185
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38225.13537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.09915163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.223153
X-RAY DIFFRACTIONr_chiral_restr0.0810.2140
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.2412
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2616
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6991.5560
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0992876
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.533359
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2234.5308
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 41 -
Rwork0.278 798 -
obs--100 %

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