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- PDB-9ayp: Mycolicibacterium smegmatis ClpS with bound Co2+ -

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Basic information

Entry
Database: PDB / ID: 9ayp
TitleMycolicibacterium smegmatis ClpS with bound Co2+
ComponentsATP-dependent Clp protease adapter protein ClpS
KeywordsPROTEIN BINDING / proteolysis / adaptor
Function / homologyATP-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 / protein catabolic process / peptidase activity / proteolysis / : / ATP-dependent Clp protease adapter protein ClpS
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 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 8, 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
B: ATP-dependent Clp protease adapter protein ClpS
A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,54011
Polymers18,0442
Non-polymers4969
Water2,864159
1
B: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3767
Polymers9,0221
Non-polymers3546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1644
Polymers9,0221
Non-polymers1423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.578, 52.145, 54.575
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

#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)
Strain: ATCC 700084 / mc(2)155 / Gene: clpS, MSMEG_4910 / Plasmid: pET22b / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / References: UniProt: A0R1X7
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#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.: 159 / Source method: isolated from a natural source / Formula: H2O
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: 2.03 Å3/Da / Density % sol: 39.52 %
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 soak: 0.1 M HEPES pH 7.5, 40% PEG3350, 5 mM CoCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.99→30.44 Å / Num. obs: 18251 / % possible obs: 97.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 11.94 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.033 / Rrim(I) all: 0.066 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 5.16 / Num. unique obs: 419 / CC1/2: 0.946 / Rpim(I) all: 0.119 / Rrim(I) all: 0.185 / % possible all: 81

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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: 1.99→30.44 Å / SU ML: 0.1611 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.4683
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1867 851 4.66 %
Rwork0.1633 17400 -
obs0.1646 18251 94.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.9 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 9 159 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431236
X-RAY DIFFRACTIONf_angle_d0.82231685
X-RAY DIFFRACTIONf_chiral_restr0.0398186
X-RAY DIFFRACTIONf_plane_restr0.0022212
X-RAY DIFFRACTIONf_dihedral_angle_d12.0593435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.120.2127650.17582225X-RAY DIFFRACTION70.94
2.12-2.280.23651340.16462974X-RAY DIFFRACTION95.07
2.28-2.510.20322070.17132995X-RAY DIFFRACTION100
2.51-2.870.2506930.16983147X-RAY DIFFRACTION99.97
2.87-3.620.19871380.16523088X-RAY DIFFRACTION99.97
3.62-30.440.14342140.14962971X-RAY DIFFRACTION98.21

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