5AF3 | pdb_00005af3

X-RAY CRYSTAL STRUCTURE OF RV2018 FROM MYCOBACTERIUM TUBERCULOSIS

• PDB DOI: https://doi.org/10.2210/pdb5AF3/pdb

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


• Deposited: 2015-01-18 Released: 2016-01-27 
• Deposition Author(s): Holton, S.J., Wilmanns, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Crystal Structure and DNA Binding Ability of Myco Tuberculosis Vapbc49 Anti-Toxin Protein Bacterium

Holton, S.J., Pogenberg, V., Iborra, V., Wilmanns, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 52.47 kDa 
• Atom Count: 3,599 
• Modeled Residue Count: 428 
• Deposited Residue Count: 482 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VAPBC49	A, B	241	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for O53464 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53464  Go to UniProtKB:  O53464

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.935	α = 90
b = 81.935	β = 90
c = 75.361	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-27 
Deposition Author(s): Holton, S.J., Wilmanns, M.

Revision History  

• Version 1.0: 2016-01-27
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other