4ZYR

Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)

• PDB DOI: https://doi.org/10.2210/pdb4ZYR/pdb

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


• Deposited: 2015-05-22 Released: 2015-07-29 
• Deposition Author(s): Kumar, H., Finer-Moore, J.S., Kaback, H.R., Stroud, R.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.278 
• R-Value Work: 0.259 
• R-Value Observed: 0.260 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 94.79 kDa 
• Atom Count: 6,241 
• Modelled Residue Count: 772 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactose permease	A, B	417	Escherichia coli K-12	Mutation(s): 2  Gene Names: lacY, b0343, JW0334 Membrane Entity: Yes
UniProt
Find proteins for P02920 (Escherichia coli (strain K12)) Explore P02920  Go to UniProtKB:  P02920

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	D [auth A], F [auth B]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
9PG	C [auth A], E [auth B]	4-nitrophenyl alpha-D-galactopyranoside C12 H15 N O8 IFBHRQDFSNCLOZ-IIRVCBMXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 0.278 
• R-Value Work: 0.259 
• R-Value Observed: 0.260 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.15	α = 90
b = 121.99	β = 90
c = 266.09	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Kumar, H., Finer-Moore, J.S., Kaback, H.R., Stroud, R.M.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R37GM024485
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK069463
National Science Foundation (NSF, United States)	United States	MCB-1129551

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2015-08-05
  Changes: Database references
• Version 1.2: 2015-08-12
  Changes: Derived calculations
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.6: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary