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- PDB-9b1p: Mycolicibacterium smegmatis ClpS with TrpSer dipeptide and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 9b1p
TitleMycolicibacterium smegmatis ClpS with TrpSer dipeptide and 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: 1.75 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 13, 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
F: ATP-dependent Clp protease adapter protein ClpS
G: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,59011
Polymers36,3174
Non-polymers2737
Water4,179232
1
A: ATP-dependent Clp protease adapter protein ClpS
F: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2665
Polymers18,1592
Non-polymers1073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-23 kcal/mol
Surface area4750 Å2
MethodPISA
2
B: ATP-dependent Clp protease adapter protein ClpS
G: ATP-dependent Clp protease adapter protein ClpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3256
Polymers18,1592
Non-polymers1664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-34 kcal/mol
Surface area4740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.313, 52.600, 54.096
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: 9079.263 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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

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 TrpSer peptide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 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→14.9 Å / Num. obs: 14280 / % possible obs: 93 % / Redundancy: 5.5 % / Biso Wilson estimate: 20.52 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.019 / Rrim(I) all: 0.046 / Net I/σ(I): 35.5
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 393 / CC1/2: 0.882 / Rpim(I) all: 0.237 / Rrim(I) all: 0.449 / % possible all: 53.1

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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→14.87 Å / SU ML: 0.1937 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6807
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1889 658 4.63 %
Rwork0.1712 13551 -
obs0.1721 14209 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.3 Å2
Refinement stepCycle: LAST / Resolution: 1.75→14.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 7 232 1498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00681303
X-RAY DIFFRACTIONf_angle_d0.85421778
X-RAY DIFFRACTIONf_chiral_restr0.0622195
X-RAY DIFFRACTIONf_plane_restr0.0098222
X-RAY DIFFRACTIONf_dihedral_angle_d16.4195454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.880.29051000.24371855X-RAY DIFFRACTION65.17
1.88-2.070.29331190.20952850X-RAY DIFFRACTION98.61
2.07-2.370.24461460.18172886X-RAY DIFFRACTION99.9
2.37-2.980.21121250.17192928X-RAY DIFFRACTION99.9
2.98-14.870.13861680.15023032X-RAY DIFFRACTION99.88

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