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- PDB-4yka: The structure of Agrobacterium tumefaciens ClpS2 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4yka
TitleThe structure of Agrobacterium tumefaciens ClpS2 in complex with L-tyrosinamide
ComponentsATP-dependent Clp protease adapter protein ClpS 2
KeywordsPROTEIN BINDING / N-end rule / Protease adaptor
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
L-TYROSINAMIDE / ATP-dependent Clp protease adapter protein ClpS 2
Similarity search - Component
Biological speciesAgrobacterium fabrum (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.801 Å
AuthorsStein, B. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049224 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Structure / Year: 2016
Title: Structural Basis of an N-Degron Adaptor with More Stringent Specificity.
Authors: Stein, B.J. / Grant, R.A. / Sauer, R.T. / Baker, T.A.
History
DepositionMar 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Feb 10, 2016Group: Database references
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 2
B: ATP-dependent Clp protease adapter protein ClpS 2
C: ATP-dependent Clp protease adapter protein ClpS 2
D: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,84411
Polymers46,8354
Non-polymers1,0097
Water82946
1
A: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9853
Polymers11,7091
Non-polymers2762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8892
Polymers11,7091
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0814
Polymers11,7091
Non-polymers3723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ATP-dependent Clp protease adapter protein ClpS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8892
Polymers11,7091
Non-polymers1801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.945, 92.648, 94.918
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 2


Mass: 11708.688 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria)
Strain: C58 / ATCC 33970 / Gene: clpS2, Atu2232, AGR_C_4060 / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (DE3) / References: UniProt: Q8UD95
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-TYC / L-TYROSINAMIDE


Type: L-peptide COOH carboxy terminus / Mass: 180.204 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H12N2O2
#4: 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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2.2M Ammonium Sulfate 0.2M Sodium Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.801→34.133 Å / Num. obs: 13019 / % possible obs: 99.7 % / Redundancy: 12.5 % / Biso Wilson estimate: 45.06 Å2 / Rsym value: 0.161 / Net I/σ(I): 15.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJM

4yjm


Resolution: 2.801→34.133 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2564 618 4.75 %
Rwork0.1867 --
obs0.1899 13019 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.801→34.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 67 46 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032753
X-RAY DIFFRACTIONf_angle_d0.673706
X-RAY DIFFRACTIONf_dihedral_angle_d10.4651036
X-RAY DIFFRACTIONf_chiral_restr0.025421
X-RAY DIFFRACTIONf_plane_restr0.003470
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8015-3.08320.30761760.23632982X-RAY DIFFRACTION99
3.0832-3.5290.25311640.19793057X-RAY DIFFRACTION100
3.529-4.44460.23031360.16653105X-RAY DIFFRACTION100
4.4446-34.13580.2581420.18183257X-RAY DIFFRACTION100

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