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- PDB-9b10: Mycolicibacterium smegmatis ClpS with TyrArg dipeptide and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9b10
TitleMycolicibacterium smegmatis ClpS with TyrArg dipeptide and Mg2+
ComponentsATP-dependent Clp protease adapter protein ClpS
KeywordsPROTEIN BINDING / proteolysis / adaptor
Function / homology
Function and homology information


protein catabolic process / peptidase activity / proteolysis
Similarity search - Function
ATP-dependent Clp protease adaptor protein ClpS / Adaptor protein ClpS, core / ATP-dependent Clp protease adaptor protein ClpS / Ribosomal protein L7/L12, C-terminal/adaptor protein ClpS-like
Similarity search - Domain/homology
ARGININE / NICKEL (II) ION / TRIETHYLENE GLYCOL / TYROSINE / ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsPresloid, C.J. / Jiang, J. / Beardslee, P.C. / Anderson, H.R. / Swayne, T.M. / Schmitz, K.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM104316 United States
CitationJournal: Mol.Microbiol. / Year: 2025
Title: ClpS Directs Degradation of N-Degron Substrates With Primary Destabilizing Residues in Mycolicibacterium smegmatis.
Authors: Presloid, C.J. / Jiang, J. / Kandel, P. / Anderson, H.R. / Beardslee, P.C. / Swayne, T.M. / Schmitz, K.R.
History
DepositionMar 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,45818
Polymers18,0442
Non-polymers1,41416
Water5,837324
1
A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6368
Polymers9,0221
Non-polymers6147
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,82210
Polymers9,0221
Non-polymers8009
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.438, 52.765, 54.004
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 9022.167 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: clpS, MSMEG_4910 / Plasmid: pET22b / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / References: UniProt: A0R1X7

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Non-polymers , 8 types, 340 molecules

#2: Chemical ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 12% PEG3350, 5 mM NiCl2 cryo: 0.1 M HEPES pH 7.5, 40% PEG3350, 5 mM MgCl2, 2.5 mM TyrArg dipeptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.28→37.74 Å / Num. obs: 38356 / % possible obs: 98.8 % / Redundancy: 8.5 % / Biso Wilson estimate: 9.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rpim(I) all: 0.013 / Rrim(I) all: 0.04 / Net I/σ(I): 58.9
Reflection shellResolution: 1.28→1.3 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 8.85 / Num. unique obs: 1632 / CC1/2: 0.977 / Rpim(I) all: 0.073 / Rrim(I) all: 0.178 / % possible all: 86.6

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→37.74 Å / SU ML: 0.0966 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 14.6293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1549 1856 4.85 %
Rwork0.1406 36411 -
obs0.1413 38267 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.26 Å2
Refinement stepCycle: LAST / Resolution: 1.28→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1250 0 40 324 1614
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671381
X-RAY DIFFRACTIONf_angle_d0.89711880
X-RAY DIFFRACTIONf_chiral_restr0.0616204
X-RAY DIFFRACTIONf_plane_restr0.01235
X-RAY DIFFRACTIONf_dihedral_angle_d14.9259519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.21121370.16582384X-RAY DIFFRACTION86.37
1.31-1.350.18561360.15712728X-RAY DIFFRACTION96.27
1.35-1.390.18391250.15312785X-RAY DIFFRACTION99.76
1.39-1.440.21061510.15072792X-RAY DIFFRACTION99.9
1.44-1.50.17021530.14192806X-RAY DIFFRACTION99.83
1.5-1.570.14731400.13172802X-RAY DIFFRACTION99.9
1.57-1.650.16761490.13952827X-RAY DIFFRACTION99.93
1.65-1.760.16341560.14172808X-RAY DIFFRACTION99.9
1.76-1.890.16341490.14792811X-RAY DIFFRACTION99.93
1.89-2.080.14311200.1332875X-RAY DIFFRACTION99.97
2.08-2.380.14331460.12912853X-RAY DIFFRACTION100
2.38-30.15231220.13522930X-RAY DIFFRACTION99.97
3-37.740.1391720.14473010X-RAY DIFFRACTION99.97

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