2BI0 | pdb_00002bi0

RV0216, A conserved hypothetical protein from Mycobacterium tuberculosis that is essential for bacterial survival during infection, has a double hotdogfold

• PDB DOI: https://doi.org/10.2210/pdb2BI0/pdb

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


• Deposited: 2005-01-20 Released: 2005-04-25 
• Deposition Author(s): Castell, A., Johansson, P., Unge, T., Jones, T.A., Backbro, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor), 0.173 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Literature

Rv0216, a Conserved Hypothetical Protein from Mycobacterium Tuberculosis that is Essential for Bacterial Survival During Infection, Has a Double Hotdog Fold

Castell, A., Johansson, P., Unge, T., Jones, T.A., Backbro, K.

(2005) Protein Sci 14: 1850

• PubMed: 15987908 
• DOI: https://doi.org/10.1110/ps.051442305
• Primary Citation Related Structures: 
  2BI0


• PubMed Abstract: 
  

  The Mycobacterium tuberculosis genome contains about 4000 genes, of which approximately a third code for proteins of unknown function or are classified as conserved hypothetical proteins. We have determined the three-dimensional structure of one of these, the rv0216 gene product, which has been shown to be essential for M. tuberculosis growth in vivo. The structure exhibits the greatest similarity to bacterial and eukaryotic hydratases that catalyse the R-specific hydration of 2-enoyl coenzyme A. However, only part of the catalytic machinery is conserved in Rv0216 and it showed no activity for the substrate crotonyl-CoA. The structure of Rv0216 allows us to assign new functional annotations to a family of seven other M. tuberculosis proteins, a number if which are essential for bacterial survival during infection and growth.

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Organizational Affiliation: 
• Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Sweden.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 35.98 kDa 
• Atom Count: 2,805 
• Modeled Residue Count: 330 
• Deposited Residue Count: 337 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN RV0216	A	337	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for P96398 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore P96398  Go to UniProtKB:  P96398

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor), 0.173 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.75	α = 90
b = 78.75	β = 90
c = 180.309	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
RSPS	phasing
MLPHARE	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-25 
Deposition Author(s): Castell, A., Johansson, P., Unge, T., Jones, T.A., Backbro, K.

Revision History  

• Version 1.0: 2005-04-25
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Other, Structure summary