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- PDB-6pba: Structure of ClpC1-NTD -

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Basic information

Entry
Database: PDB / ID: 6pba
TitleStructure of ClpC1-NTD
ComponentsATP-dependent Clp protease ATP-binding subunit ClpC1
KeywordsCHAPERONE / ClpC1-NTD / ATPase / Clp protease
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 amino terminal domain, pathogenicity island component / : ...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 amino terminal domain, pathogenicity island component / : / Clp, repeat (R) domain / Clp repeat (R) domain profile. / Clp, N-terminal domain superfamily / ClpA/B family / Clp ATPase, C-terminal / AAA domain (Cdc48 subfamily) / C-terminal, D2-small domain, of ClpB protein / C-terminal, D2-small domain, of ClpB protein / 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
ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsAbad-Zapatero, C. / Wolf, N.M.
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
DepositionJun 13, 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: ATP-dependent Clp protease ATP-binding subunit ClpC1


Theoretical massNumber of molelcules
Total (without water)17,5291
Polymers17,5291
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.530, 59.120, 58.790
Angle α, β, γ (deg.)90.00, 97.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-261-

HOH

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Components

#1: Protein ATP-dependent Clp protease ATP-binding subunit ClpC1


Mass: 17529.131 Da / Num. of mol.: 1 / Fragment: N-terminal domain (UNP residues 1-145)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES, pH 6.0, 40% PEG400, 5% PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.77→40 Å / Num. obs: 13940 / % possible obs: 99.61 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.069 / Net I/σ(I): 41.5
Reflection shellResolution: 1.77→1.93 Å / Rmerge(I) obs: 0.513 / Num. unique obs: 780 / CC1/2: 0.815 / Rsym value: 0.447

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CN8

6cn8


Resolution: 1.77→35.4 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.419 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22294 745 5.1 %RANDOM
Rwork0.19539 ---
obs0.19677 13940 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.709 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å20 Å2-1.09 Å2
2---0.54 Å20 Å2
3----2.54 Å2
Refinement stepCycle: 1 / Resolution: 1.77→35.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1174 0 0 81 1255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131225
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171220
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6261637
X-RAY DIFFRACTIONr_angle_other_deg1.3691.5662816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2075153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19321.38565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115222
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9611511
X-RAY DIFFRACTIONr_chiral_restr0.0840.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8332.979609
X-RAY DIFFRACTIONr_mcbond_other2.8342.972608
X-RAY DIFFRACTIONr_mcangle_it4.0254.445760
X-RAY DIFFRACTIONr_mcangle_other4.0224.453761
X-RAY DIFFRACTIONr_scbond_it4.0523.687615
X-RAY DIFFRACTIONr_scbond_other4.0493.691616
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5645.256876
X-RAY DIFFRACTIONr_long_range_B_refined8.81537.2611365
X-RAY DIFFRACTIONr_long_range_B_other8.81237.2941366
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.773→1.819 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 57 -
Rwork0.288 973 -
obs--96.44 %

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