3QE7

Crystal Structure of Uracil Transporter--UraA

• PDB DOI: https://doi.org/10.2210/pdb3QE7/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2011-01-20 Released: 2011-03-23 
• Deposition Author(s): Lu, F.R., Li, S., Yan, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.303 
• R-Value Work: 0.248 
• R-Value Observed: 0.251 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.51 kDa 
• Atom Count: 3,030 
• Modelled Residue Count: 407 
• Deposited Residue Count: 429 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil permease	A	429	Escherichia coli K-12	Mutation(s): 0  Gene Names: uraA, b2497, JW2482 Membrane Entity: Yes
UniProt
Find proteins for P0AGM7 (Escherichia coli (strain K12)) Explore P0AGM7  Go to UniProtKB:  P0AGM7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BNG	C [auth A]	nonyl beta-D-glucopyranoside C15 H30 O6 QFAPUKLCALRPLH-UXXRCYHCSA-N
URA	B [auth A]	URACIL C4 H4 N2 O2 ISAKRJDGNUQOIC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.303 
• R-Value Work: 0.248 
• R-Value Observed: 0.251 
• Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.76	α = 90
b = 96.76	β = 90
c = 251.95	γ = 120

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Lu, F.R., Li, S., Yan, N.

Revision History  

• Version 1.0: 2011-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Structure summary