4Q6U

Crystal structure of a putative uncharacterized protein from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4Q6U/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Mycobacterium tuberculosis CDC1551
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-23 Released: 2014-06-18 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Literature

Mycobacterium tuberculosis Rv3651 is a triple sensor-domain protein.

Abendroth, J., Frando, A., Phan, I.Q., Staker, B.L., Myler, P.J., Edwards, T.E., Grundner, C.

(2018) Protein Sci 27: 568-572

• PubMed: 29119630 
• DOI: https://doi.org/10.1002/pro.3343
• Primary Citation of Related Structures:  
  4Q6U


• PubMed Abstract: 
  

  The genome of the human pathogen Mycobacterium tuberculosis (Mtb) encodes ∼4,400 proteins, but one third of them have unknown functions. We solved the crystal structure of Rv3651, a hypothetical protein with no discernible similarity to proteins with known function. Rv3651 has a three-domain architecture that combines one cGMP-specific phosphodiesterases, adenylyl cyclases and FhlA (GAF) domain and two Per-ARNT-Sim (PAS) domains. GAF and PAS domains are sensor domains that are typically linked to signaling effector molecules. Unlike these sensor-effector proteins, Rv3651 is an unusual sensor domain-only protein with highly divergent sequence. The structure suggests that Rv3651 integrates multiple different signals and serves as a scaffold to facilitate signal transfer.

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Organizational Affiliation: 

Beryllium Discovery, Bainbridge Island, Washington.

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: 78.99 kDa 
• Atom Count: 5,360 
• Modelled Residue Count: 642 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	353	Mycobacterium tuberculosis CDC1551	Mutation(s): 0  Gene Names: MT3753
UniProt
Find proteins for I6YCP0 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6YCP0  Go to UniProtKB:  I6YCP0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1PE	C [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.218 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M34Q6U

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.62	α = 90
b = 73.02	β = 90
c = 82.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2018-03-07
  Changes: Database references