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- PDB-6ucr: Structure of ClpC1-NTD L92S L96P -

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Basic information

Entry
Database: PDB / ID: 6ucr
TitleStructure of ClpC1-NTD L92S L96P
ComponentsNegative regulator of genetic competence ClpC/mecB
KeywordsCHAPERONE / ClpC1-NTD / ATPase / Mycobacterium tuberculosis
Function / homology
Function and homology information


protein folding chaperone / peptidoglycan-based cell wall / protein homodimerization activity / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol
Similarity search - Function
Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : ...Double Clp-N motif / Clp, N-terminal domain / UVR domain / UVR domain profile. / ClpA/B, conserved site 1 / Chaperonins clpA/B signature 1. / ClpA/ClpB, AAA lid domain / AAA lid domain / Clp repeat (R) N-terminal domain / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / AAA domain (Cdc48 subfamily) / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Negative regulator of genetic competence ClpC/mecB / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAbad-Zapatero, C. / Wolf, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1U19AI142735-01 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structure of the N-terminal domain of ClpC1 in complex with the antituberculosis natural product ecumicin reveals unique binding interactions.
Authors: Wolf, N.M. / Lee, H. / Zagal, D. / Nam, J.W. / Oh, D.C. / Lee, H. / Suh, J.W. / Pauli, G.F. / Cho, S. / Abad-Zapatero, C.
History
DepositionSep 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Negative regulator of genetic competence ClpC/mecB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5462
Polymers17,4871
Non-polymers591
Water1,838102
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-1 kcal/mol
Surface area8420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.137, 63.350, 68.305
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 Negative regulator of genetic competence ClpC/mecB


Mass: 17487.008 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-145) / Mutation: L92S, L96P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: H37Rv / Gene: clpC, ERS007720_03236 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0U0SI28, UniProt: P9WPC9*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.36 Å3/Da / Density % sol: 47.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES, pH 7.5, 10% PEG8000, 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2019
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 7594 / % possible obs: 96.4 % / Redundancy: 12.7 % / CC1/2: 0.995 / Rpim(I) all: 0.028 / Rrim(I) all: 0.1 / Net I/σ(I): 56.1
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 27.2 / Num. unique obs: 376 / CC1/2: 0.99 / Rpim(I) all: 0.068 / Rrim(I) all: 0.253

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Processing

Software
NameClassification
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CN8

6cn8


Resolution: 2.3→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.23697 357 4.7 %
Rwork0.18642 --
obs0.18899 7202 96.2 %
Displacement parametersBiso mean: 23.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1193 0 4 102 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411214
X-RAY DIFFRACTIONf_angle_d1.79721636
X-RAY DIFFRACTIONf_chiral_restr0.0808187
X-RAY DIFFRACTIONf_plane_restr0.0068215
X-RAY DIFFRACTIONf_dihedral_angle_d18.4043730

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