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- PDB-9az5: Mycolicibacterium smegmatis ClpS with bound Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9az5
TitleMycolicibacterium smegmatis ClpS with bound Mg2+
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 / NICKEL (II) ION / ATP-dependent Clp protease adapter protein ClpS
Function and homology information
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.47 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 10, 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)18,3039
Polymers18,0442
Non-polymers2587
Water5,026279
1
A: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1735
Polymers9,0221
Non-polymers1514
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)9,1294
Polymers9,0221
Non-polymers1073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.367, 52.289, 54.605
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)
Gene: clpS, MSMEG_4910 / Plasmid: pET22b / Production host: Escherichia coli B (bacteria) / Strain (production host): ER2566 / References: UniProt: A0R1X7
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-NI / NICKEL (II) ION


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


Mass: 18.015 Da / Num. of mol.: 279 / 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: 39.47 %
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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.47→30.43 Å / Num. obs: 24656 / % possible obs: 95.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 12.37 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.017 / Rrim(I) all: 0.052 / Net I/σ(I): 23.9
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 1.14 / Num. unique obs: 652 / CC1/2: 0.698 / Rpim(I) all: 0.472 / Rrim(I) all: 0.696

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PHENIX1.20.1_4487refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→27.3 Å / SU ML: 0.1742 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1845 1191 4.84 %
Rwork0.1489 23412 -
obs0.1507 24603 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.83 Å2
Refinement stepCycle: LAST / Resolution: 1.47→27.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1229 0 10 279 1518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011291
X-RAY DIFFRACTIONf_angle_d1.13781764
X-RAY DIFFRACTIONf_chiral_restr0.0829198
X-RAY DIFFRACTIONf_plane_restr0.0212221
X-RAY DIFFRACTIONf_dihedral_angle_d15.4776463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.47-1.530.38141010.29831877X-RAY DIFFRACTION70.44
1.53-1.60.25061410.19172508X-RAY DIFFRACTION94.78
1.6-1.680.21221370.15772609X-RAY DIFFRACTION97.69
1.68-1.790.21161540.15092647X-RAY DIFFRACTION99.36
1.79-1.930.20891230.15062700X-RAY DIFFRACTION100
1.93-2.120.19471060.12632739X-RAY DIFFRACTION99.96
2.12-2.430.18841590.12992690X-RAY DIFFRACTION100
2.43-3.060.17111050.14412789X-RAY DIFFRACTION99.97
3.06-27.30.1451650.14652853X-RAY DIFFRACTION99.97

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