6KKK

Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward open conformation (H115A mutant)

• PDB DOI: https://doi.org/10.2210/pdb6KKK/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2019-07-26 Released: 2020-07-29 
• Deposition Author(s): Xiao, Q.J., Deng, D.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 137.19 kDa 
• Atom Count: 8,493 
• Modelled Residue Count: 1,143 
• Deposited Residue Count: 1,269 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar efflux transporter	A, B, C	423	Escherichia coli K-12	Mutation(s): 1  Gene Names: sotB, ydeA, b1528, JW1521 Membrane Entity: Yes
UniProt
Find proteins for P31122 (Escherichia coli (strain K12)) Explore P31122  Go to UniProtKB:  P31122

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG (Subject of Investigation/LOI)	D [auth A], E [auth B], F [auth C]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.267 
• R-Value Work: 0.231 
• R-Value Observed: 0.234 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 261.618	α = 90
b = 61.822	β = 93.42
c = 122.463	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-29 
Deposition Author(s): Xiao, Q.J., Deng, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	China	YFA052700
National Science Foundation (China)	China	JQ007

Revision History  

• Version 1.0: 2020-07-29
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references, Structure summary
• Version 1.2: 2022-03-23
  Changes: Author supporting evidence, Database references