2YIZ

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.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 21897938 Search on PubMed
DOI: https://doi.org/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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8VK10
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COA Query on COA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D]	E [auth A], J [auth B], O [auth C], S [auth D]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain S [auth D]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C] mmCIF format, chain T [auth D]	F [auth A], K [auth B], P [auth C], T [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain T [auth D]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain Q [auth C] MOL2 format, chain Q [auth C] mmCIF format, chain Q [auth C]	Q [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain Q [auth C] Interactions & Density Focus chain Q [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain R [auth C] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C]	N [auth B], R [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain N [auth B] Focus chain R [auth C] Interactions & Density Focus chain N [auth B] Focus chain R [auth C]

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 = 94.302	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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-12

Deposition Author(s):

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
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description