2YIZ

X-ray structure of Mycobacterium tuberculosis Dodecin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


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

  • DOI: 10.1039/c1cc12929e
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Philipps-Universität Marburg, Fachbereich Chemie, Hans-Meerwein-Strasse, 35032 Marburg, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DODECINA, B, C, D69Mycobacterium tuberculosis H37RvMutation(s): 0 
UniProt
Find proteins for Q8VK10 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore Q8VK10 
Go to UniProtKB:  Q8VK10
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VK10
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
O [auth C],
S [auth D]		COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N		 Ligand Interaction
FMN
Query on FMN
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C],
T [auth D]		FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
Q [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
N [auth B],
R [auth C]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.302α = 90
b = 94.302β = 90
c = 230.907γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-12
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Derived calculations