2YJ0

X-ray structure of chemically engineered Mycobacterium tuberculosis Dodecin

PDB DOI: https://doi.org/10.2210/pdb2YJ0/pdb

Classification: FLAVOPROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

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: 2.40 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220

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: 55.46 kDa
Atom Count: 4,001
Modelled Residue Count: 407
Deposited Residue Count: 414
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, E A, B, C, D, E, F	69	Mycobacterium tuberculosis H37Rv	Mutation(s): 1
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 BA [auth F] SDF format, chain L [auth B] SDF format, chain X [auth E] SDF format, chain H [auth A] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain BA [auth F] MOL2 format, chain L [auth B] MOL2 format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain BA [auth F] mmCIF format, chain L [auth B] mmCIF format, chain X [auth E] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	BA [auth F] H [auth A] L [auth B] Q [auth C] T [auth D] BA [auth F], H [auth A], L [auth B], Q [auth C], T [auth D], X [auth E]	COENZYME A C₂₁ H₃₆ N₇ O₁₆ P₃ S RGJOEKWQDUBAIZ-IBOSZNHHSA-N		Interactions Focus chain BA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain BA [auth F] Focus chain H [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain X [auth E]
420 Query on 420 Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain S [auth D] SDF format, chain W [auth E] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain AA [auth F] MOL2 format, chain S [auth D] MOL2 format, chain W [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain AA [auth F] mmCIF format, chain S [auth D] mmCIF format, chain W [auth E] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	AA [auth F] G [auth A] K [auth B] P [auth C] S [auth D] AA [auth F], G [auth A], K [auth B], P [auth C], S [auth D], W [auth E]	N-[2-({[5-(DIMETHYLAMINO)NAPHTHALEN-1-YL]SULFONYL}AMINO)ETHYL]-2-IODOACETAMIDE C₁₆ H₂₀ I N₃ O₃ S QDHGMMDEGVINBU-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E] Interactions & Density Focus chain AA [auth F] Focus chain G [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain S [auth D] Focus chain W [auth E]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain CA [auth F] SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D]	CA [auth F] I [auth A] M [auth B] R [auth C] U [auth D] CA [auth F], I [auth A], M [auth B], R [auth C], U [auth D], Y [auth E]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain I [auth A] Focus chain M [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain Y [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain Z [auth E]	V [auth D], Z [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain V [auth D] Focus chain Z [auth E]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B]	J [auth A], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94	α = 90
b = 103.8	β = 90
c = 82.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	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: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary