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- PDB-9b06: Mycolicibacterium smegmatis ClpS with LeuThr dipeptide and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9b06
TitleMycolicibacterium smegmatis ClpS with LeuThr 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
(2S)-2-amino-4-methylpentanal / NICKEL (II) ION / THREONINE / ATP-dependent Clp protease adapter protein ClpS
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 11, 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)18,73811
Polymers18,0442
Non-polymers6939
Water5,224290
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A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3395
Polymers9,0221
Non-polymers3174
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)9,3986
Polymers9,0221
Non-polymers3765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.244, 52.707, 54.044
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 , 5 types, 299 molecules

#2: Chemical ChemComp-LCZ / (2S)-2-amino-4-methylpentanal


Type: peptide-like / Mass: 115.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13NO
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4910 / Plasmid: pET22b / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566
#3: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C4H9NO3
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Gene: MSMEG_4910 / Plasmid: pET22b / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 12% PEG3350, 5 mM NiCl2 cryo: 0.1M HEPES pH 7.5, 40% PEG3350, 5 mM MgCl2, 2.5 mM LeuThr peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→25.62 Å / Num. obs: 14242 / % possible obs: 92.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.93 Å2 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 29.7
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 385 / CC1/2: 0.833 / Rpim(I) all: 0.247 / Rrim(I) all: 0.491 / % possible all: 52.5

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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: 1.75→25.62 Å / SU ML: 0.1677 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1886 655 4.61 %
Rwork0.1405 13542 -
obs0.1429 14197 92.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.49 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1239 0 5 290 1534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841309
X-RAY DIFFRACTIONf_angle_d0.91371790
X-RAY DIFFRACTIONf_chiral_restr0.067201
X-RAY DIFFRACTIONf_plane_restr0.0081226
X-RAY DIFFRACTIONf_dihedral_angle_d13.9305471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.890.2648960.18251870X-RAY DIFFRACTION65.77
1.89-2.070.25171210.14422831X-RAY DIFFRACTION97.98
2.08-2.370.19041450.13562873X-RAY DIFFRACTION100
2.38-2.990.1971240.14282940X-RAY DIFFRACTION99.97
2.99-25.620.16091690.13433028X-RAY DIFFRACTION99.91

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