Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D6  (3D View)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content

• Total Structure Weight: 83.84 kDa 
• Atom Count: 6304 
• Residue Count: 792 
• Unique protein chains: 1

4JDY

Crystal structure of Rv2606c

• DOI: 10.2210/pdb4JDY/pdb

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


• Deposited: 2013-02-25 Released: 2013-05-22 
• Deposition Author(s): Kim, S., Kim, K.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Literature

Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase

Kim, S., Kim, K.-J.

(2013) Biochem Biophys Res Commun 

• PubMed: 23643787 
• DOI: 10.1016/j.bbrc.2013.04.068
• Primary Citation of Related Structures:  
  4JDY


• PubMed Abstract: 
  

Tuberculosis is a lethal infectious disease caused by Mycobacterium tuberculosis. We determined the crystal structure of Rv2606c, a potential pyridoxal biosynthesis lyase (PdxS), from M. tuberculosis H37Rv at 1.8 Å resolution. The overall structure of the protein, composed of a (β/α)8-barrel and two small 310-helices, was quite similar to those of other PdxS proteins. A glycerol molecule was observed to be bound at the active site of the Rv2606c structure through interactions with the conserved residues of Asp29 and Lys86, providing information regarding the potential active site and the substrate-binding environment of the protein. The interface for Rv2606c dodecamerization, which is primarily mediated by salt bridges and hydrophobic interactions, was quite different from those of other PdxS proteins. Furthermore, we observed that the Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as PdxS and PdxT in M. tuberculosis.

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Organizational Affiliation: 

School of Life Science and Biotechnology, Kyungpook National University, Republic of Korea.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyridoxal biosynthesis lyase PdxS	A, B, C	264	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: pdxS, Rv2606c, MT2681, MTCY1A10.27 EC: 4.3.3.6
Find proteins for P9WII9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WII9  Go to UniProtKB:  P9WII9

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.211 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.752	α = 90
b = 126.08	β = 90
c = 180.816	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-02-25 
• Released Date: 2013-05-22 
Deposition Author(s): Kim, S., Kim, K.-J.

Revision History 

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description