7YD4

Crystal structure of an N terminal truncated secreted protein, Rv0398c from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb7YD4/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-07-03 Released: 2023-06-28 
• Deposition Author(s): Saha, R., Mukherjee, S., Singh, B.K., Weiss, M.S., De, S., Das, A.K.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 

Literature

Crystal structure of a mycobacterial secretory protein Rv0398c and in silico prediction of its export pathway

Saha, R., Mukherjee, S., Singh, B., De, S., Weiss, M.S., Das, A.K.

(2023) Biochem Biophys Res Commun 672: 45-53

• DOI: https://doi.org/10.1016/j.bbrc.2023.06.029

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 19.27 kDa 
• Atom Count: 1,371 
• Modelled Residue Count: 179 
• Deposited Residue Count: 185 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Possible secreted protein	A	185	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv0398c
UniProt
Find proteins for P95206 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P95206  Go to UniProtKB:  P95206

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.229 
• R-Value Work: 0.185 
• R-Value Observed: 0.190 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.881	α = 90
b = 73.463	β = 90
c = 103.724	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Saha, R., Mukherjee, S., Singh, B.K., Weiss, M.S., De, S., Das, A.K.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release