6VJ5 | pdb_00006vj5

Structure of PE25-PPE41(A124L) in complex with EspG5 chaperone from the type VII (ESX-5) secretion system

• PDB DOI: https://doi.org/10.2210/pdb6VJ5/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Mycobacterium tuberculosis H37Rv, Mycobacterium marinum M
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-01-14 Released: 2021-01-27 
• Deposition Author(s): Williamson, Z.A., Korotkov, K.V.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.254 (Depositor) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Molecular basis of diverse substrate recognition by EspG5 chaperone from mycobacterial ESX-5 Type VII Secretion System.

Williamson, Z.A., Korotkova, N., Korotkov, K.V.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 65.36 kDa 
• Atom Count: 4,416 
• Modeled Residue Count: 545 
• Deposited Residue Count: 595 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PE-PGRS family protein PE25	A	101	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: PE25, Rv2431c, LH57_13295
UniProt
Find proteins for I6X486 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6X486  Go to UniProtKB:  I6X486

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PPE family protein PPE41	B	194	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: PPE41, Rv2430c, LH57_13290
UniProt
Find proteins for Q79FE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore Q79FE1  Go to UniProtKB:  Q79FE1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ESX-5 secretion-associated protein EspG5	C	300	Mycobacterium marinum M	Mutation(s): 0  Gene Names: espG5, MMAR_2676
UniProt
Find proteins for B2HSU5 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HSU5  Go to UniProtKB:  B2HSU5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth B], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.254 (Depositor) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.02	α = 90
b = 139.02	β = 90
c = 170.57	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Currently 6VJ5 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2021-01-27 
Deposition Author(s): Williamson, Z.A., Korotkov, K.V.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI119022
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103486
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM110787

Revision History  

• Version 1.0: 2021-01-27
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description