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- PDB-3g1b: The structure of the M53A mutant of Caulobacter crescentus clpS p... -

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Basic information

Entry
Database: PDB / ID: 3g1b
TitleThe structure of the M53A mutant of Caulobacter crescentus clpS protease adaptor protein in complex with WLFVQRDSKE peptide
Components
  • 10-residue peptide
  • ATP-dependent Clp protease adapter protein clpS
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 / Resolution: 1.448 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 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: 10-residue peptide
D: 10-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4366
Polymers22,3874
Non-polymers492
Water5,927329
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-16 kcal/mol
Surface area8950 Å2
MethodPISA
2
A: ATP-dependent Clp protease adapter protein clpS
C: 10-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2183
Polymers11,1942
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-4 kcal/mol
Surface area4900 Å2
MethodPISA
3
B: ATP-dependent Clp protease adapter protein clpS
D: 10-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2183
Polymers11,1942
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area610 Å2
ΔGint-4 kcal/mol
Surface area5030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.597, 54.017, 44.891
Angle α, β, γ (deg.)90.000, 110.480, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 9884.229 Da / Num. of mol.: 2 / Mutation: M53A
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 10-residue peptide


Mass: 1309.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 1.7045 Å3/Da / Density % sol: 27.838091 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M bis-tris pH 5.5, 0.2 M MgCl2, 20% 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: Dec 17, 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: 1.45→100 Å / Num. obs: 23780 / % possible obs: 88.7 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.057 / Χ2: 1.125 / Net I/σ(I): 34.292
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.45-1.53.10.08112670.32447.7
1.5-1.563.90.07720620.43877.2
1.56-1.635.40.07725300.56394.8
1.63-1.725.50.0725310.62895.3
1.72-1.835.50.06325890.73196.5
1.83-1.975.50.05725670.86296.1
1.97-2.175.50.05225651.10495.9
2.17-2.485.50.05225951.35996.8
2.48-3.125.50.05326371.70597.4
3.12-1005.20.06124372.72788.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementStarting model: 3dnj

3dnj


Resolution: 1.448→22.725 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.885 / SU ML: 0.12 / σ(F): 1.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 1949 8.2 %
Rwork0.173 --
obs0.175 23763 88.54 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.262 Å2 / ksol: 0.459 e/Å3
Displacement parametersBiso max: 72.02 Å2 / Biso mean: 19.862 Å2 / Biso min: 9.06 Å2
Baniso -1Baniso -2Baniso -3
1-2.276 Å20 Å2-0.962 Å2
2---2.158 Å2-0 Å2
3----0.118 Å2
Refinement stepCycle: LAST / Resolution: 1.448→22.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2724 0 2 329 3055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062754
X-RAY DIFFRACTIONf_angle_d0.8184944
X-RAY DIFFRACTIONf_chiral_restr0.058213
X-RAY DIFFRACTIONf_plane_restr0.004421
X-RAY DIFFRACTIONf_dihedral_angle_d14.924683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.448-1.4840.173610.15672178242
1.484-1.5240.218810.1431128120963
1.524-1.5690.1761290.1371506163587
1.569-1.620.1561390.1451671181094
1.62-1.6780.1931290.1471705183495
1.678-1.7450.1961390.1531684182396
1.745-1.8240.1741340.1581729186397
1.824-1.920.1961540.1661673182796
1.92-2.0410.1971780.151644182296
2.041-2.1980.1831660.141687185396
2.198-2.4190.161800.1461680186097
2.419-2.7690.151590.1481713187297
2.769-3.4860.1731670.1521669183695
3.486-22.7280.21330.1961604173788

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