8IBO

Crystal structure of Wild-Type Mycobacterium tuberculosis ClpC1 N-terminal domain in complex with Lassomycin

• PDB DOI: https://doi.org/10.2210/pdb8IBO/pdb

• Classification: CHAPERONE
• Organism(s): Mycobacterium tuberculosis, Lentzea kentuckyensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-02-10 Released: 2023-09-20 
• Deposition Author(s): Jagdev, M.K., Vasudevan, D.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.236 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

Crystal structure of the N-terminal domain of MtClpC1 in complex with the anti-mycobacterial natural peptide Lassomycin

Jagdev, M.K., Tompa, D.R., Ling, L.L., Peoples, A.J., Dandapat, J., Mohapatra, C., Lewis, K., Vasudevan, D.

(2023) Int J Biol Macromol 253: 126771

• DOI: https://doi.org/10.1016/j.ijbiomac.2023.126771

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 17.72 kDa 
• Atom Count: 1,347 
• Modelled Residue Count: 158 
• Deposited Residue Count: 158 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Negative regulator of genetic competence ClpC/mecB	A	142	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: clpC_1
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC9  Go to UniProtKB:  P9WPC9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lassomycin	B [auth C]	16	Lentzea kentuckyensis	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.236 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.431	α = 90
b = 58.468	β = 90
c = 64.763	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Jagdev, M.K., Vasudevan, D.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations