2YIZ | pdb_00002yiz

X-ray structure of Mycobacterium tuberculosis Dodecin

• PDB DOI: https://doi.org/10.2210/pdb2YIZ/pdb

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


• Deposited: 2011-05-17 Released: 2011-10-12 
• Deposition Author(s): Vinzenz, X., Grosse, W., Linne, U., Meissner, B., Essen, L.-O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.197 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Chemical Engineering of Mycobacterium Tuberculosis Dodecin Hybrids.

Vinzenz, X., Grosse, W., Linne, U., Meissner, B., Essen, L.-O.

(2011) Chem Commun (Camb) 47: 11071

• PubMed: 21897938 
• DOI: https://doi.org/10.1039/c1cc12929e
• Primary Citation Related Structures: 
  2YIZ, 2YJ0


• PubMed Abstract: 
  

  The suitability for chemical engineering of the highly symmetrical Mycobacterium tuberculosis dodecin was investigated, its inner cavity providing a large compartment shields introduced compounds from bulk solvent. Hybrids were obtained by S-alkylation of cysteine mutants and characterized by spectroscopic methods, including the crystal structures of wild type and biohybrid dodecins.

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Organizational Affiliation: 
• Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Strasse, 35032 Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Macromolecule Content 

• Total Structure Weight: 35.57 kDa 
• Atom Count: 2,670 
• Modeled Residue Count: 272 
• Deposited Residue Count: 276 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DODECIN	A, B, C, D	69	Mycobacterium tuberculosis H37Rv	Mutation(s): 0
UniProt
Find proteins for Q8VK10 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)) Explore Q8VK10  Go to UniProtKB:  Q8VK10

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
COA	E [auth A], J [auth B], O [auth C], S [auth D]	COENZYME A C21 H36 N7 O16 P3 S RGJOEKWQDUBAIZ-IBOSZNHHSA-N
FMN	F [auth A], K [auth B], P [auth C], T [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
TRS	Q [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.197 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.302	α = 90
b = 94.302	β = 90
c = 230.907	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Vinzenz, X., Grosse, W., Linne, U., Meissner, B., Essen, L.-O.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description