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- PDB-3g19: The structure of the Caulobacter crescentus clpS protease adaptor... -

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Basic information

Entry
Database: PDB / ID: 3g19
TitleThe structure of the Caulobacter crescentus clpS protease adaptor protein in complex with LLL tripeptide
Components
  • ATP-dependent Clp protease adapter protein clpS
  • LLL tripeptide
KeywordsPEPTIDE BINDING PROTEIN / adaptor / protein-peptide complex / peptide-binding protein
Function / homology
Function and homology information


protein catabolic process / 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 speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.849 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
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands

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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
C: LLL tripeptide


Theoretical massNumber of molelcules
Total (without water)10,3022
Polymers10,3022
Non-polymers00
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-5 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.658, 34.419, 71.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 9944.347 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Strain: CB15 / Gene: CC_2467, clpS / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5I0
#2: Protein/peptide LLL tripeptide


Mass: 357.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 1.71663 Å3/Da / Density % sol: 28.348003 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 10, 2008 / Details: Varimax-HR
RadiationMonochromator: Varimax-HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 5661 / % possible obs: 87.1 % / Redundancy: 6 % / Biso Wilson estimate: 13.78 Å2 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.043 / Χ2: 1.062 / Net I/av σ(I): 39.645 / Net I/σ(I): 16.2 / Num. measured all: 33923
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.85-1.923.10.1163250.86551.4
1.92-1.994.50.1144611.06474.7
1.99-2.085.10.0965111.23781.2
2.08-2.196.20.0876131.2295.6
2.19-2.335.90.0734831.04475.5
2.33-2.516.80.0536320.90899.1
2.51-2.766.80.0466410.89699.2
2.76-3.166.70.046601.01799.5
3.16-3.996.50.0346141.19392.5
3.99-506.20.0287211.11999.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.849→22.388 Å / Occupancy max: 1 / Occupancy min: 0.52 / FOM work R set: 0.849 / SU ML: 0.22 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.212 563 10 %
Rwork0.185 --
obs0.188 5629 87.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.543 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso max: 40.72 Å2 / Biso mean: 13.429 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1--0.439 Å2-0 Å20 Å2
2---1.034 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.849→22.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms715 0 0 127 842
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002728
X-RAY DIFFRACTIONf_angle_d0.59985
X-RAY DIFFRACTIONf_chiral_restr0.042112
X-RAY DIFFRACTIONf_plane_restr0.003127
X-RAY DIFFRACTIONf_dihedral_angle_d17.661269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.849-2.0350.2231060.19965107168
2.035-2.3290.2241310.1951181131283
2.329-2.9340.2331600.1861435159599
2.934-22.3890.1911660.1751485165197

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