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- PDB-3gq0: The structure of the Caulobacter crescentus clpS protease adaptor... -

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Basic information

Entry
Database: PDB / ID: 3gq0
TitleThe structure of the Caulobacter crescentus clpS protease adaptor protein - apo structure with no peptide
ComponentsATP-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 / SYNCHROTRON / Resolution: 2.066 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 1.0Apr 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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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


Theoretical massNumber of molelcules
Total (without water)19,8892
Polymers19,8892
Non-polymers00
Water82946
1
A: ATP-dependent Clp protease adapter protein clpS


Theoretical massNumber of molelcules
Total (without water)9,9441
Polymers9,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent Clp protease adapter protein clpS


Theoretical massNumber of molelcules
Total (without water)9,9441
Polymers9,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.667, 38.479, 62.560
Angle α, β, γ (deg.)90.000, 88.420, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 39:95 or resseq 97:119 )
21chain B and (resseq 39:95 or resseq 97:119 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA39 - 955 - 61
12LYSLYSASPASPAA97 - 11963 - 85
21SERSERGLUGLUBB39 - 955 - 61
22LYSLYSASPASPBB97 - 11963 - 85

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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

Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 5.5
Details: 0.1 M bis-tris pH 5.5, 0.025 M MgCl2, 14% 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: Varimax-HR
RadiationMonochromator: crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 7983 / % possible obs: 98.2 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.141 / Χ2: 1.311 / Net I/σ(I): 22.816
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.148.20.4353930.45494.5
2.14-2.188.50.4083890.48197
2.18-2.2290.3793710.47597.6
2.22-2.269.30.3344000.55998
2.26-2.31100.3614100.54396.7
2.31-2.3710.20.3143770.54398.4
2.37-2.4210.80.2983940.63198.5
2.42-2.4910.90.2833870.64598
2.49-2.5611.20.2744040.75698.1
2.56-2.6511.30.2643960.77399
2.65-2.7411.30.2193950.94698
2.74-2.8511.20.1984131.16999
2.85-2.9811.30.1953851.19598.7
2.98-3.1411.30.1684041.58798.8
3.14-3.3311.20.144001.81499
3.33-3.59110.1324102.20399.3
3.59-3.95110.1184132.53599
3.95-4.5210.60.1064022.69699.3
4.52-5.710.90.1034202.49399.1
5.7-5010.50.0954202.64598.8

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Processing

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

3dnj


Resolution: 2.066→32.772 Å / Occupancy max: 1 / Occupancy min: 0.99 / FOM work R set: 0.758 / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 0.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.264 366 4.69 %random
Rwork0.221 ---
obs0.223 7799 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.384 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso max: 119.47 Å2 / Biso mean: 37.454 Å2 / Biso min: 14.59 Å2
Baniso -1Baniso -2Baniso -3
1-3.953 Å20 Å213.821 Å2
2---9.034 Å20 Å2
3---5.082 Å2
Refinement stepCycle: LAST / Resolution: 2.066→32.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 0 46 1400
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041382
X-RAY DIFFRACTIONf_angle_d0.7121873
X-RAY DIFFRACTIONf_chiral_restr0.046210
X-RAY DIFFRACTIONf_plane_restr0.003243
X-RAY DIFFRACTIONf_dihedral_angle_d14.506504
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A658X-RAY DIFFRACTIONPOSITIONAL
12B658X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.066-2.3650.2981230.2542288241189
2.365-2.9790.2841230.2322512263596
2.979-32.7760.2461200.2062633275399

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