4KV3

Ubiquitin-like domain of the Mycobacterium tuberculosis type VII secretion system protein EccD1 as maltose-binding protein fusion

• PDB DOI: https://doi.org/10.2210/pdb4KV3/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Escherichia coli K-12, Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-05-22 Released: 2014-04-09 
• Deposition Author(s): Korotkov, K.V., Evans, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system.

Wagner, J.M., Chan, S., Evans, T.J., Kahng, S., Kim, J., Arbing, M.A., Eisenberg, D., Korotkov, K.V.

(2016) BMC Struct Biol 16: 5-5

• PubMed: 26922638 
• DOI: https://doi.org/10.1186/s12900-016-0056-6
• Primary Citation of Related Structures:  
  4KK7, 4KV2, 4KV3, 5CYU


• PubMed Abstract: 
  

  The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system.

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Organizational Affiliation: 

Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.75 kDa 
• Atom Count: 7,434 
• Modelled Residue Count: 912 
• Deposited Residue Count: 922 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chimera fusion protein of ESX-1 secretion system protein eccD1 and Maltose-binding periplasmic protein	A, B	461	Escherichia coli K-12, Mycobacterium tuberculosis H37Rv This entity is chimeric	Mutation(s): 3
UniProt
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 125.68	α = 90
b = 125.68	β = 90
c = 124.49	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-04-09 
Deposition Author(s): Korotkov, K.V., Evans, T.J.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release
  
• Version 1.1: 2016-03-23
  Changes: Database references
• Version 1.2: 2017-07-26
  Changes: Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary