6NKB

Crystal structure of Dethiobiotin Synthetase from Mycobacterium tuberculosis in complex with 2'-deoxycytidine diphosphate

• PDB DOI: https://doi.org/10.2210/pdb6NKB/pdb

• Classification: TRANSFERASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2020-01-15 
• Deposition Author(s): Thompson, A.P., Polyak, S.W., Wegener, K.L., Bruning, J.B.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 

Literature

Crystal structure of Dethiobiotin Synthetase from Mycobacterium tuberculosis in complex with 2'-deoxycytidine diphosphate

Thompson, A.P., Polyak, S.W., Wegener, K.L., Bruning, J.B.

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)

Biological Assembly Evidence: homology

Biological Assembly 2  

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

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

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 94.76 kDa 
• Atom Count: 7,345 
• Modelled Residue Count: 907 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent dethiobiotin synthetase BioD	A, B, C, D	233	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: bioD, Rv1570, MTCY336.33c EC: 6.3.3.3
UniProt
Find proteins for P9WPQ5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPQ5  Go to UniProtKB:  P9WPQ5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YYY (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C], J [auth D]	DEOXYCYTIDINE DIPHOSPHATE C9 H15 N3 O10 P2 FTDHDKPUHBLBTL-SHYZEUOFSA-N
MG (Subject of Investigation/LOI)	F [auth A], I [auth C], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.265 
• R-Value Work: 0.209 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.8	α = 90
b = 105.2	β = 90
c = 154.19	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-15 
Deposition Author(s): Thompson, A.P., Polyak, S.W., Wegener, K.L., Bruning, J.B.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History  

• Version 1.0: 2020-01-15
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Derived calculations