5E27

The structure of Resuscitation Promoting Factor B from M. tuberculosis reveals unexpected ubiquitin-like domains

• PDB DOI: https://doi.org/10.2210/pdb5E27/pdb

• Classification: CELL ADHESION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-09-30 Released: 2015-11-18 
• Deposition Author(s): Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R.
• Funding Organization(s): EU

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains.

Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R.

(2015) Biochim Biophys Acta 1860: 445-451

• PubMed: 26549874 
• DOI: https://doi.org/10.1016/j.bbagen.2015.11.001
• Primary Citation of Related Structures:  
  5E27


• PubMed Abstract: 
  

  RpfB is a key factor in resuscitation from dormancy of Mycobacterium tuberculosis. This protein is a cell-wall glycosidase, which cleaves cell-wall peptidoglycan. RpfB is structurally complex and is composed of three types of domains, including a catalytic, a G5 and three DUF348 domains. Structural information is currently limited to a portion of the protein including only the catalytic and G5 domains. To gain insights into the structure and function of all domains we have undertaken structural investigations on a large protein fragment containing all three types of domains that constitute RpfB (RpfB3D).

---

Organizational Affiliation: 

Institute of Biostructures and Bioimaging, CNR, via Mezzocannone 16, Napoli, Italy.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.81 kDa 
• Atom Count: 3,387 
• Modelled Residue Count: 446 
• Deposited Residue Count: 496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Resuscitation-promoting factor RpfB	A, B	248	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  rpfB, ABI38_15460, BN1303_02209, ERS024750_01702, ERS024751_02059, ERS024758_02236, ERS024764_01503, ERS094182_03333, ERS124362_01696, ERS124821_03131, ERS124823_03398, ERS124824_03090, ERS124825_03322, ERS124826_03034, ERS124827_03238, ERS124828_02982, ERS124829_03081, ERS124830_03164, ERS124832_03150, IQ42_14370, IQ45_14195, IQ47_14175, IQ48_14250, IU12_14990, IU13_14360, IU15_14665, IU16_14305, IU21_14520, T209_14145
UniProt
Find proteins for P9WG29 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG29  Go to UniProtKB:  P9WG29

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.376	α = 90
b = 126.99	β = 90
c = 86.286	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-11-18 
Deposition Author(s): Ruggiero, A., Squeglia, F., Romano, M., Vitagliano, L., De Simone, A., Berisio, R.

---

Funding Organization	Location	Grant Number
EU		GA 609535

Revision History  

• Version 1.0: 2015-11-18
  Type: Initial release
  
• Version 1.1: 2015-12-23
  Changes: Database references