6MGF

untagged, wild-type LptB in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb6MGF/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-09-13 Released: 2019-09-18 
• Deposition Author(s): Mandler, M.D., Owens, T.W., Ruiz, N., Kahne, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 

Literature

Bypassing the requirement for coupling of ATP binding and hydrolysis in the lipopolysaccharide ABC transporte

Simpson, B., Ruiz, N.

Not Published 

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 27.88 kDa 
• Atom Count: 1,936 
• Modelled Residue Count: 240 
• Deposited Residue Count: 241 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipopolysaccharide export system ATP-binding protein LptB	A	241	Escherichia coli K-12	Mutation(s): 0  Gene Names: lptB, yhbG, b3201, JW3168 EC: 3.6.3
UniProt
Find proteins for P0A9V1 (Escherichia coli (strain K12)) Explore P0A9V1  Go to UniProtKB:  P0A9V1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CZJ	D [auth A]	(3s,5s,7s)-N-{7-[(3-O-carbamoyl-6-deoxy-5-methyl-4-O-methyl-beta-D-gulopyranosyl)oxy]-4-hydroxy-8-methyl-2-oxo-2H-1-ben zopyran-3-yl}tricyclo[3.3.1.1~3,7~]decane-1-carboxamide C30 H38 N2 O10 SFCPIJFPMNEBLW-GGTPUZHSSA-N
ADP	C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.205 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.742	α = 90
b = 34.767	β = 100.07
c = 62.897	γ = 90

Software Package:

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

Structure Validation

Currently 6MGF does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2019-09-18 
Deposition Author(s): Mandler, M.D., Owens, T.W., Ruiz, N., Kahne, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM066174
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI081059

Revision History  

• Version 1.0: 2019-09-18
  Type: Initial release
  
• Version 1.1: 2019-12-18
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary