[English] 日本語
Yorodumi
- PDB-6pbs: Structure of ClpC1-NTD in complex with Ecumicin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pbs
TitleStructure of ClpC1-NTD in complex with Ecumicin
Components
  • ATP-dependent Clp protease ATP-binding subunit ClpC1
  • ecumicin
KeywordsCHAPERONE/ANTIBIOTIC / ClpC1-NTD / Ecumicin / ATPase / Mycobacterium tuberculosis / CHAPERONE-ANTIBIOTIC complex
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
ecumicin / ACETATE ION / ATP-dependent Clp protease ATP-binding subunit ClpC1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Nonomuraea sp. MJM5123 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 2.0Dec 30, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_molecule / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_auth_evidence / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / space_group / space_group_symop / struct_asym / struct_conf / struct_conn / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_fragment / _entity.pdbx_number_of_molecules / _entity.src_method / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_molecule_features.prd_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_R_Free_selection_details / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_starting_model / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_ref_seq.pdbx_strand_id
Description: Chirality error
Details: Peptide ligand was found to contain a chirality error based on small molecule structure of ligand. The resolution of this structure wasn't good enough to catch the erros.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 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
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ATP-dependent Clp protease ATP-binding subunit ClpC1
I: ATP-dependent Clp protease ATP-binding subunit ClpC1
C: ATP-dependent Clp protease ATP-binding subunit ClpC1
W: ATP-dependent Clp protease ATP-binding subunit ClpC1
Y: ATP-dependent Clp protease ATP-binding subunit ClpC1
e: ATP-dependent Clp protease ATP-binding subunit ClpC1
B: ATP-dependent Clp protease ATP-binding subunit ClpC1
G: ATP-dependent Clp protease ATP-binding subunit ClpC1
K: ATP-dependent Clp protease ATP-binding subunit ClpC1
M: ATP-dependent Clp protease ATP-binding subunit ClpC1
O: ATP-dependent Clp protease ATP-binding subunit ClpC1
T: ATP-dependent Clp protease ATP-binding subunit ClpC1
D: ecumicin
E: ecumicin
F: ecumicin
H: ecumicin
J: ecumicin
L: ecumicin
N: ecumicin
P: ecumicin
Q: ecumicin
R: ecumicin
S: ecumicin
U: ecumicin
V: ecumicin
X: ecumicin
Z: ecumicin
a: ecumicin
b: ecumicin
c: ecumicin
d: ecumicin
f: ecumicin
g: ecumicin
h: ecumicin
i: ecumicin
j: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)250,36456
Polymers249,18336
Non-polymers1,18120
Water10,359575
1
A: ATP-dependent Clp protease ATP-binding subunit ClpC1
D: ecumicin
E: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8835
Polymers20,7653
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
I: ATP-dependent Clp protease ATP-binding subunit ClpC1
Q: ecumicin
R: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8835
Polymers20,7653
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ATP-dependent Clp protease ATP-binding subunit ClpC1
J: ecumicin
L: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
W: ATP-dependent Clp protease ATP-binding subunit ClpC1
d: ecumicin
f: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0017
Polymers20,7653
Non-polymers2364
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
Y: ATP-dependent Clp protease ATP-binding subunit ClpC1
g: ecumicin
h: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9426
Polymers20,7653
Non-polymers1773
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
e: ATP-dependent Clp protease ATP-binding subunit ClpC1
i: ecumicin
j: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8835
Polymers20,7653
Non-polymers1182
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
B: ATP-dependent Clp protease ATP-binding subunit ClpC1
F: ecumicin
H: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
G: ATP-dependent Clp protease ATP-binding subunit ClpC1
N: ecumicin
P: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
K: ATP-dependent Clp protease ATP-binding subunit ClpC1
S: ecumicin
U: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
M: ATP-dependent Clp protease ATP-binding subunit ClpC1
V: ecumicin
X: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
O: ATP-dependent Clp protease ATP-binding subunit ClpC1
Z: ecumicin
a: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
T: ATP-dependent Clp protease ATP-binding subunit ClpC1
b: ecumicin
c: ecumicin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8244
Polymers20,7653
Non-polymers591
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.063, 130.342, 112.562
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

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


Mass: 17529.131 Da / Num. of mol.: 12
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: Protein/peptide ...
ecumicin


Type: Cyclic peptide / Class: Antibiotic / Mass: 1618.051 Da / Num. of mol.: 24 / Source method: obtained synthetically / Source: (synth.) Nonomuraea sp. MJM5123 (bacteria) / References: ecumicin
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M calcium acetate hydrate, 0.1 M Tris, pH 7.0, 20% PEG3000

-
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: Apr 23, 2017
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: 2.5→40 Å / Num. obs: 79421 / % possible obs: 98.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.638 / Num. unique obs: 3828 / Rpim(I) all: 0.364 / Rrim(I) all: 0.786

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6pba

6pba


Resolution: 2.5→40 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.257 --
Rwork0.18 --
obs-77925 97.9 %
Displacement parametersBiso mean: 64.05 Å2
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13588 0 2816 575 16979

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more