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- PDB-3gq1: The structure of the caulobacter crescentus clpS protease adaptor... -

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Basic information

Entry
Database: PDB / ID: 3gq1
TitleThe structure of the caulobacter crescentus clpS protease adaptor protein in complex with a WLFVQRDSKE decapeptide
Components
  • ATP-dependent Clp protease adapter protein clpS
  • WLFVQRDSKE peptide
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: 1.496 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 23, 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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: ATP-dependent Clp protease adapter protein clpS
C: WLFVQRDSKE peptide
D: WLFVQRDSKE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5325
Polymers22,5084
Non-polymers241
Water3,747208
1
A: ATP-dependent Clp protease adapter protein clpS
C: WLFVQRDSKE peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2783
Polymers11,2542
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-6 kcal/mol
Surface area5610 Å2
MethodPISA
2
B: ATP-dependent Clp protease adapter protein clpS
D: WLFVQRDSKE peptide


Theoretical massNumber of molelcules
Total (without water)11,2542
Polymers11,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-4 kcal/mol
Surface area5660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.533, 53.905, 45.039
Angle α, β, γ (deg.)90.00, 110.33, 90.00
Int Tables number4
Space group name H-MP1211

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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: CC_2467, clpS / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5I0
#2: Protein/peptide WLFVQRDSKE peptide


Mass: 1309.469 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


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.83 Å3/Da / Density % sol: 27.47 %
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: 1.5416 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: 1.5416 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 21297 / % possible obs: 87.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.046 / Χ2: 0.969 / Net I/σ(I): 47.864
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.556.10.1311090.39846.1
1.55-1.6270.11119110.42879.1
1.62-1.697.30.09321940.44389.9
1.69-1.787.30.07721740.48691
1.78-1.897.30.06622320.57492
1.89-2.047.40.05322540.69993.1
2.04-2.247.30.0523030.97694.5
2.24-2.567.40.04623221.23895.4
2.56-3.237.40.04323761.67497.2
3.23-5070.0424222.21397.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.496→31.444 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.889 / SU ML: 0.13 / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 1078 5.07 %
Rwork0.16 --
obs0.161 21279 87.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.122 Å2 / ksol: 0.469 e/Å3
Displacement parametersBiso max: 86.04 Å2 / Biso mean: 33.408 Å2 / Biso min: 16.17 Å2
Baniso -1Baniso -2Baniso -3
1--13.675 Å2-0 Å2-2.83 Å2
2---18.487 Å2-0 Å2
3----19.451 Å2
Refinement stepCycle: LAST / Resolution: 1.496→31.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 1 208 3223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083056
X-RAY DIFFRACTIONf_angle_d0.9655519
X-RAY DIFFRACTIONf_chiral_restr0.071236
X-RAY DIFFRACTIONf_plane_restr0.006465
X-RAY DIFFRACTIONf_dihedral_angle_d15.323777
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.496-1.5640.167610.1311403146448
1.564-1.6470.1841380.1332451258985
1.647-1.750.1761290.1392626275591
1.75-1.8850.1811370.142641277892
1.885-2.0750.1591450.1332693283893
2.075-2.3750.1751520.1322741289395
2.375-2.9920.1761660.1382775294197
2.992-31.4510.1681500.1742871302197

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