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- PDB-6cn8: High-resolution structure of ClpC1-NTD binding to Rufomycin-I -

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Basic information

Entry
Database: PDB / ID: 6cn8
TitleHigh-resolution structure of ClpC1-NTD binding to Rufomycin-I
Components
  • ATP-dependent Clp protease ATP-binding subunit ClpC1
  • Rufomycin I
KeywordsCHAPERONE/ANTIBIOTIC / Mycobacterium tuberculosis / rufomycin I / macrocyclic peptide / ClpC1-NTD / Chaperone / ATP-dependent protease / CHAPERONE-ANTIBIOTIC complex / ATPase AAA+ / natural product
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
Rufomycin I / PHOSPHATE ION / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Streptomyces atratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsAbad-Zapatero, C. / Wolf, N.W.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
Rural Development AdministrationPJ01328403 Korea, Republic Of
Rural Development AdministrationPJ01319101 Korea, Republic Of
CitationJournal: Acs Infect Dis. / Year: 2019
Title: High-Resolution Structure of ClpC1-Rufomycin and Ligand Binding Studies Provide a Framework to Design and Optimize Anti-Tuberculosis Leads.
Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J. ...Authors: Wolf, N.M. / Lee, H. / Choules, M.P. / Pauli, G.F. / Phansalkar, R. / Anderson, J.R. / Gao, W. / Ren, J. / Santarsiero, B.D. / Lee, H. / Cheng, J. / Jin, Y.Y. / Ho, N.A. / Duc, N.M. / Suh, J.W. / Abad-Zapatero, C. / Cho, S.
History
DepositionMar 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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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
B: Rufomycin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,92211
Polymers18,5932
Non-polymers3299
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-81 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.758, 109.758, 109.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-208-

NA

21A-209-

NA

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 17529.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal domain (UNP residues 1-145) / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: clpC1, Rv3596c, MTCY07H7B.26 / Plasmid: pET30a+ / Production host: Escherichia coli (E. coli) / References: UniProt: P9WPC9
#2: Protein/peptide Rufomycin I


Type: Cyclic peptide / Class: Antimicrobial / Mass: 1064.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces atratus (bacteria) / References: Rufomycin I

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Non-polymers , 4 types, 215 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.96 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.2 M sodium/potassium phosphate, pH 6.2, 2.5 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0781 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 25, 2017
RadiationMonochromator: double crystal Si(111) with bimorphic K-B mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.4→19.403 Å / Num. obs: 44919 / % possible obs: 99.9 % / Redundancy: 38 % / Biso Wilson estimate: 18.12 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.099 / Net I/σ(I): 58.7
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 24.1 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4391 / CC1/2: 0.84 / Rrim(I) all: 1.362 / % possible all: 99.73

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3WDB

3wdb


Resolution: 1.4→19.403 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.97
RfactorNum. reflection% reflection
Rfree0.1848 2359 5.26 %
Rwork0.1588 --
obs0.1602 44888 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→19.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 13 211 1473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081294
X-RAY DIFFRACTIONf_angle_d1.1121754
X-RAY DIFFRACTIONf_dihedral_angle_d18.142485
X-RAY DIFFRACTIONf_chiral_restr0.075204
X-RAY DIFFRACTIONf_plane_restr0.005224
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4002-1.42870.25021210.2312441X-RAY DIFFRACTION100
1.4287-1.45980.231420.20132443X-RAY DIFFRACTION100
1.4598-1.49370.20171340.16772465X-RAY DIFFRACTION100
1.4937-1.53110.18921330.16422447X-RAY DIFFRACTION100
1.5311-1.57240.17311450.15242473X-RAY DIFFRACTION100
1.5724-1.61870.20361540.15292444X-RAY DIFFRACTION100
1.6187-1.67090.1731170.15342487X-RAY DIFFRACTION100
1.6709-1.73060.20351380.15332454X-RAY DIFFRACTION100
1.7306-1.79980.18631500.14412479X-RAY DIFFRACTION100
1.7998-1.88170.18681340.14522470X-RAY DIFFRACTION100
1.8817-1.98080.17071250.14692514X-RAY DIFFRACTION100
1.9808-2.10480.14851510.14312500X-RAY DIFFRACTION100
2.1048-2.26710.16041620.14252482X-RAY DIFFRACTION100
2.2671-2.49480.15691260.13712545X-RAY DIFFRACTION100
2.4948-2.85480.17611420.15992534X-RAY DIFFRACTION100
2.8548-3.5930.1761350.16772600X-RAY DIFFRACTION100
3.593-19.40450.22191500.17222751X-RAY DIFFRACTION100

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