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- PDB-3dnj: The structure of the Caulobacter crescentus ClpS protease adaptor... -

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Basic information

Entry
Database: PDB / ID: 3dnj
TitleThe structure of the Caulobacter crescentus ClpS protease adaptor protein in complex with a N-end rule peptide
Components
  • ATP-dependent Clp protease adapter protein clpS
  • synthetic N-end rule peptide
KeywordsPEPTIDE BINDING PROTEIN / ADAPTOR / PROTEIN-PEPTIDE COMPLEX
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 Å
AuthorsWang, K. / Roman-Hernandez, G. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
CitationJournal: Mol.Cell / Year: 2008
Title: The molecular basis of N-end rule recognition.
Authors: Wang, K.H. / Roman-Hernandez, G. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionJul 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: 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 / 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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: synthetic N-end rule peptide
D: synthetic N-end rule peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4865
Polymers22,4624
Non-polymers241
Water5,098283
1
B: ATP-dependent Clp protease adapter protein clpS
D: synthetic N-end rule peptide


Theoretical massNumber of molelcules
Total (without water)11,2312
Polymers11,2312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-4 kcal/mol
Surface area5030 Å2
MethodPISA
2
A: ATP-dependent Clp protease adapter protein clpS
C: synthetic N-end rule peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2553
Polymers11,2312
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-4 kcal/mol
Surface area4990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.693, 53.974, 44.824
Angle α, β, γ (deg.)90.00, 110.39, 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: clpS, CC_2467 / Plasmid: PET23B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A5I0
#2: Protein/peptide synthetic N-end rule peptide


Mass: 1286.433 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED
#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.: 283 / 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: 1.7 Å3/Da / Density % sol: 27.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5 0.2 M MGCL2 13% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 51120 / % possible obs: 95.6 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.078 / Χ2: 1.167 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.15-1.192.50.19436830.28569.5
1.19-1.243.90.20448490.31791
1.24-1.36.30.18753360.37899.9
1.3-1.366.80.15353120.417100
1.36-1.4570.12353460.511100
1.45-1.567.10.10153360.728100
1.56-1.727.10.08953470.991100
1.72-1.977.10.08453471.578100
1.97-2.4870.07853662.582100
2.48-506.40.06151982.73695.2

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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
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1R60 chain C

1r60


Resolution: 1.15→14.876 Å / Occupancy max: 1 / Occupancy min: 0.21 / FOM work R set: 0.938 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.159 2538 4.97 %RANDOM
Rwork0.135 ---
all0.1362 ---
obs0.136 51076 95.62 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.155 Å2 / ksol: 0.447 e/Å3
Displacement parametersBiso max: 48.51 Å2 / Biso mean: 12.129 Å2 / Biso min: 2.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.843 Å2-0 Å2-1.039 Å2
2---1.739 Å2-0 Å2
3----2.148 Å2
Refinement stepCycle: LAST / Resolution: 1.15→14.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3016 0 1 283 3300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063063
X-RAY DIFFRACTIONf_angle_d0.8765548
X-RAY DIFFRACTIONf_chiral_restr0.062236
X-RAY DIFFRACTIONf_plane_restr0.005470
X-RAY DIFFRACTIONf_dihedral_angle_d14.713796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.15-1.1720.138950.1161822191765
1.172-1.1960.1581090.1142131224076
1.196-1.2220.1411170.1142531264890
1.222-1.250.1571500.1072780293098
1.25-1.2820.1311620.127812943100
1.282-1.3160.1341560.09527972953100
1.316-1.3550.1341490.09428062955100
1.355-1.3990.1251380.09628222960100
1.399-1.4490.1381450.09628252970100
1.449-1.5070.1271360.09828042940100
1.507-1.5750.1191470.128122959100
1.575-1.6580.141620.10928152977100
1.658-1.7620.1481630.12228122975100
1.762-1.8980.1611320.13228292961100
1.898-2.0880.1581420.12728412983100
2.088-2.3890.1521320.13528452977100
2.389-3.0060.1741720.15128172989100
3.006-14.8770.1851310.1762668279992

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