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- PDB-8ad9: Crystal structure of ClpC2 C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 8ad9
TitleCrystal structure of ClpC2 C-terminal domain
Components
  • Cyclomarin A
  • Putative ATP-dependent protease ATP-binding subunit ClpC2
KeywordsDNA BINDING PROTEIN / ClpC2 / CymA / C-terminal domain / Transcription factor
Function / homologyClp amino terminal domain, pathogenicity island component / Clp repeat (R) domain profile. / Clp, repeat (R) domain / Clp, N-terminal domain superfamily / cytosol / : / ACETATE ION / DI(HYDROXYETHYL)ETHER / Uncharacterized protein Rv2667
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.43 Å
AuthorsTaylor, G. / Cui, H.J. / Leodolter, J. / Giese, C. / Weber-Ban, E.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: Commun Biol / Year: 2023
Title: ClpC2 protects mycobacteria against a natural antibiotic targeting ClpC1-dependent protein degradation.
Authors: Taylor, G. / Cui, H. / Leodolter, J. / Giese, C. / Weber-Ban, E.
History
DepositionJul 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative ATP-dependent protease ATP-binding subunit ClpC2
B: Putative ATP-dependent protease ATP-binding subunit ClpC2
C: Cyclomarin A
D: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,68416
Polymers36,6874
Non-polymers99712
Water3,981221
1
A: Putative ATP-dependent protease ATP-binding subunit ClpC2
D: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8598
Polymers18,3442
Non-polymers5156
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-39 kcal/mol
Surface area7700 Å2
MethodPISA
2
B: Putative ATP-dependent protease ATP-binding subunit ClpC2
C: Cyclomarin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8258
Polymers18,3442
Non-polymers4816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-51 kcal/mol
Surface area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.582, 40.455, 59.741
Angle α, β, γ (deg.)90.000, 112.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Putative ATP-dependent protease ATP-binding subunit ClpC2 / ClpC2 / Rv2667


Mass: 17282.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-terminal SENLYF sequence is from the TEV recognition site.
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv2667, MTCY441.36 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P9WPC7
#2: Protein/peptide Cyclomarin A


Type: Peptide-like / Class: Antibiotic, Antimicrobial / Mass: 1061.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002419

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Non-polymers , 5 types, 233 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100 mM C2H3NaO2 pH 4.5, 30 % (w/v) PEG 8K, 200 mM LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→38.67 Å / Num. obs: 57672 / % possible obs: 98.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.96 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.024 / Rrim(I) all: 0.062 / Net I/σ(I): 14.9 / Num. measured all: 393155 / Scaling rejects: 44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.43-1.456.60.9241878528430.7620.3841.0032.197.9
7.83-38.675.50.05821203850.990.0280.06533.898.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WDC

3wdc


Resolution: 1.43→38.67 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2109 2842 4.93 %
Rwork0.1801 54813 -
obs0.1817 57655 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.68 Å2 / Biso mean: 28.9576 Å2 / Biso min: 15.45 Å2
Refinement stepCycle: final / Resolution: 1.43→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 209 221 2670
Biso mean--26.54 37.38 -
Num. residues----299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.450.32371460.30692716286298
1.45-1.480.25851370.26052594273195
1.48-1.510.26261180.23032645276396
1.51-1.540.22121270.22127882915100
1.54-1.570.23531470.210127572904100
1.57-1.610.22811330.195827742907100
1.61-1.650.21681360.19562736287299
1.65-1.70.22271390.190827692908100
1.7-1.750.2081420.19427492891100
1.75-1.80.22641630.200627602923100
1.8-1.870.19131520.181127392891100
1.87-1.940.16751490.18242707285698
1.94-2.030.19711260.18222615274194
2.03-2.140.21661380.19242777291599
2.14-2.270.23171300.17827992929100
2.27-2.450.22761520.18227632915100
2.45-2.690.20111430.19342774291799
2.69-3.080.18271350.18522784291999
3.08-3.880.18541350.16382711284696
3.88-38.670.22921940.161528563050100

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