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- PDB-3gw1: The structure of the Caulobacter crescentus CLPs protease adaptor... -

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Basic information

Entry
Database: PDB / ID: 3gw1
TitleThe structure of the Caulobacter crescentus CLPs protease adaptor protein in complex with FGG tripeptide
Components
  • ATP-dependent Clp protease adapter protein ClpS
  • FGG peptide
KeywordsPEPTIDE BINDING PROTEIN / adaptor / protein-peptide complex / peptide-binding protein
Function / homology
Function and homology information


protein catabolic process / peptidase activity / 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 / ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsBaker, T.A. / Roman-Hernandez, G. / Sauer, R.T. / Grant, R.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Molecular basis of substrate selection by the N-end rule adaptor protein ClpS.
Authors: Roman-Hernandez, G. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_entity_src_syn / pdbx_initial_refinement_model / struct_ref / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-dependent Clp protease adapter protein ClpS
B: ATP-dependent Clp protease adapter protein ClpS
C: FGG peptide
D: FGG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4725
Polymers20,4474
Non-polymers241
Water45025
1
A: ATP-dependent Clp protease adapter protein ClpS
C: FGG peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2483
Polymers10,2242
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-4 kcal/mol
Surface area5040 Å2
MethodPISA
2
B: ATP-dependent Clp protease adapter protein ClpS
D: FGG peptide


Theoretical massNumber of molelcules
Total (without water)10,2242
Polymers10,2242
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-4 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.599, 38.320, 62.857
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 38:119 )
211chain B and (resseq 38:119 )

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Components

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


Mass: 9944.347 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: clpS / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: A0A290MK63, UniProt: Q9A5I0*PLUS
#2: Protein/peptide FGG peptide


Mass: 279.293 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 1.625559 Å3/Da / Density % sol: 24.333721 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M bis-tris pH 5.5, 0.2 M MgCl2, 25% PEG 3350, vapor diffusion, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2009 / Details: crystal monochromator
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.36→100 Å / Num. obs: 4895 / % possible obs: 96.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.933
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.36-2.442.60.31896.8
2.44-2.492.70.37898.5
2.49-2.532.70.35698.4
2.53-2.592.80.30397
2.59-2.642.90.25998.1
2.64-2.72.80.2696.7
2.7-2.772.80.23898.1
2.77-2.8530.22996.1
2.85-2.932.90.19897.5
2.93-3.022.80.14898.8
3.02-3.132.80.13396
3.13-3.262.80.12492.4
3.26-3.412.80.10595.9
3.41-3.592.80.09295.1
3.59-3.812.80.08794.8
3.81-4.12.80.08193
4.1-4.522.80.07194.4
4.52-5.172.70.06994.9
5.17-6.512.70.06494.3
6.51-1002.70.04795.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dnj

3dnj


Resolution: 2.36→32.719 Å / Occupancy max: 1.05 / Occupancy min: 0.36 / SU ML: 0.45 / σ(F): 1.38 / Phase error: 36.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2974 221 4.52 %
Rwork0.2703 --
obs0.2717 4884 88.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.603 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 26.657 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.36→32.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 1 25 1405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041408
X-RAY DIFFRACTIONf_angle_d0.671904
X-RAY DIFFRACTIONf_dihedral_angle_d19.1512
X-RAY DIFFRACTIONf_chiral_restr0.047212
X-RAY DIFFRACTIONf_plane_restr0.003245
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A667X-RAY DIFFRACTIONPOSITIONAL
12B667X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3597-2.97270.37251010.32662128X-RAY DIFFRACTION81
2.9727-32.72230.2641200.24532535X-RAY DIFFRACTION95

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