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- PDB-2wa8: Structural basis of N-end rule substrate recognition in Escherich... -

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Basic information

Entry
Database: PDB / ID: 2wa8
TitleStructural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS - The Phe peptide structure
Components
  • ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
  • N-END RULE PEPTIDE
KeywordsPEPTIDE BINDING PROTEIN / N-END RULE / PHE PEPTIDE / CLPS / CLPA / CLPP / PEPTIDE-BINDING PROTEIN
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 / Resolution: 2.15 Å
AuthorsSchuenemann, V.J. / 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
DepositionFeb 3, 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 ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: N-END RULE PEPTIDE
C: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
D: N-END RULE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)27,1114
Polymers27,1114
Non-polymers00
Water1,63991
1
A: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
B: N-END RULE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,5562
Polymers13,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-12.5 kcal/mol
Surface area7360 Å2
MethodPQS
2
C: ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
D: N-END RULE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)13,5562
Polymers13,5562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6.5 kcal/mol
Surface area9390 Å2
MethodPQS
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 30 - 90 / Label seq-ID: 30 - 90

Dom-IDAuth asym-IDLabel asym-ID
1AA
2CC

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Components

#1: Protein ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS / CLPS - PHE-PEPTIDE COMPLEX


Mass: 12340.212 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CLPS PROTEIN FROM E. COLI AND N-END RULE PEPTIDE / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(GOLD) / References: UniProt: P0A8Q6
#2: Protein/peptide N-END RULE PEPTIDE


Mass: 1215.355 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ESCHERICHIA COLI (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.1 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 8.5 / Details: pH 8.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 10728 / % possible obs: 94 % / Observed criterion σ(I): 2.3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 6.6
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.3 / % possible all: 90.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 747 7 %RANDOM
Rwork0.225 ---
obs0.228 9909 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: 33.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.16 Å2
2--2.02 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1660 0 0 91 1751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9672284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62324.8179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.1215303
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.084157
X-RAY DIFFRACTIONr_chiral_restr0.1190.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021257
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.2844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.21189
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.2158
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.921.51033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.32321666
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it7.2583659
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.4174.5618
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A244medium positional0.020.5
2C244medium positional0.020.5
1A239loose positional0.035
2C239loose positional0.035
1A244medium thermal0.952
2C244medium thermal0.952
1A239loose thermal1.1110
2C239loose thermal1.1110
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.335 54
Rwork0.26 716

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