2G38

A PE/PPE Protein Complex from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Toward the structural genomics of complexes: Crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.

Strong, M.Sawaya, M.R.Wang, S.Phillips, M.Cascio, D.Eisenberg, D.

(2006) Proc Natl Acad Sci U S A 103: 8060-8065

  • DOI: 10.1073/pnas.0602606103
  • Primary Citation of Related Structures:  
    2G38

  • PubMed Abstract: 
  • The developing science called structural genomics has focused to date mainly on high-throughput expression of individual proteins, followed by their purification and structure determination. In contrast, the term structural biology is used to denote ...

    The developing science called structural genomics has focused to date mainly on high-throughput expression of individual proteins, followed by their purification and structure determination. In contrast, the term structural biology is used to denote the determination of structures, often complexes of several macromolecules, that illuminate aspects of biological function. Here we bridge structural genomics to structural biology with a procedure for determining protein complexes of previously unknown function from any organism with a sequenced genome. From computational genomic analysis, we identify functionally linked proteins and verify their interaction in vitro by coexpression/copurification. We illustrate this procedure by the structural determination of a previously unknown complex between a PE and PPE protein from the Mycobacterium tuberculosis genome, members of protein families that constitute approximately 10% of the coding capacity of this genome. The predicted complex was readily expressed, purified, and crystallized, although we had previously failed in expressing individual PE and PPE proteins on their own. The reason for the failure is clear from the structure, which shows that the PE and PPE proteins mate along an extended apolar interface to form a four-alpha-helical bundle, where two of the alpha-helices are contributed by the PE protein and two by the PPE protein. Our entire procedure for the identification, characterization, and structural determination of protein complexes can be scaled to a genome-wide level.


    Organizational Affiliation

    Howard Hughes Medical Institute, UCLA-Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA 90095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PE FAMILY PROTEINA, C99Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: Rv2431c
Find proteins for Q7D756 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Explore Q7D756 
Go to UniProtKB:  Q7D756
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PPE FAMILY PROTEINB, D198Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: Rv2430cPPE41LH57_13290
Find proteins for Q79FE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q79FE1 
Go to UniProtKB:  Q79FE1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
B, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.862α = 90
b = 46.758β = 90
c = 283.125γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
BOSdata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description