6GV1

Crystal structure of E.coli Multidrug/H+ antiporter MdfA in outward open conformation with bound Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Outward open conformation of a Major Facilitator Superfamily multidrug/H+antiporter provides insights into switching mechanism.

Nagarathinam, K.Nakada-Nakura, Y.Parthier, C.Terada, T.Juge, N.Jaenecke, F.Liu, K.Hotta, Y.Miyaji, T.Omote, H.Iwata, S.Nomura, N.Stubbs, M.T.Tanabe, M.

(2018) Nat Commun 9: 4005-4005


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Major Facilitator Superfamily multidrug/H+ antiporter MdfA from E.coli
A
410Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: mdfA (cmlA, cmr)
Find proteins for P0AEY8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab fragment YN1074 heavy chain
H
236N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab fragment YN1074 light chain
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.258 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 73.258α = 90.00
b = 73.258β = 90.00
c = 927.920γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyBMBF 03Z2HN21
Japan Agency for Medical Research and Development (AMED)JapanJP18am0101071j0001

Revision History 

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-10-10
    Type: Data collection, Database references, Structure summary