5IMU | pdb_00005imu

A fragment of conserved hypothetical protein Rv3899c (residues 184-410) from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb5IMU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2017-03-08 
• Deposition Author(s): Li, D.F., Gao, Y.R., Liu, Y.Y., Bi, L.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Literature

Crystal structure of Rv3899c(184-410), a hypothetical protein from Mycobacterium tuberculosis

Liu, Y.Y., Gao, Y.R., Li, D.F., Fleming, J., Li, H.L., Bi, L.J.

(2016) Acta Crystallogr F Struct Biol Commun 72: 642-645

• PubMed: 27487929 
• DOI: https://doi.org/10.1107/S2053230X16010943
• Primary Citation Related Structures: 
  5IMU


• PubMed Abstract: 
  

  Rv3899c is a hypothetical protein from Mycobacterium tuberculosis which is conserved across mycobacteria. It is predicted to be secreted and has been found in culture filtrates. It has been proposed as a potential vaccine candidate; however, its biological function is unknown. Here, the global structure of Rv3899c(184-410), a fragment of Rv3899c, is reported. The structure resembles the shell of a sea snail, and its N- and C-termini form two relatively independent compact domains: an α/β/α sandwich folding domain and an α-helix bundle domain. There are no reported protein structures for any Rv3899c homologues; this structure provides the first structural glimpse of a new protein family consisting of Rv3899c and its homologues.

---

Organizational Affiliation: 
• Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, People's Republic of China.
National Laboratory of Biomacromolecules and Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, People's Republic of China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 24.29 kDa 
• Atom Count: 1,995 
• Modeled Residue Count: 217 
• Deposited Residue Count: 227 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tat (Twin-arginine translocation) pathway signal sequence containing protein	A	227	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv3899c, LH57_21230
UniProt
Find proteins for O05446 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O05446  Go to UniProtKB:  O05446

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	B [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.155	α = 90
b = 54.973	β = 90
c = 75.807	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-03-08 
Deposition Author(s): Li, D.F., Gao, Y.R., Liu, Y.Y., Bi, L.J.

Revision History  

• Version 1.0: 2017-03-08
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references