1USK | pdb_00001usk

L-leucine-binding protein with leucine bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.252 (Depositor), 0.301 (DCC) 
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

X-Ray Structures of the Leucine-Binding Protein Illustrate Conformational Changes and the Basis of Ligand Specificity

Magnusson, U.Salopek-Sondi, B.Luck, L.A.Mowbray, S.L.

(2004) J Biological Chem 279: 8747

  • DOI: https://doi.org/10.1074/jbc.M311890200
  • Primary Citation Related Structures: 
    1USG, 1USI, 1USK

  • PubMed Abstract: 

    The periplasmic leucine-binding protein is the primary receptor for the leucine transport system in Escherichia coli. We report here the structure of an open ligand-free form solved by molecular replacement and refined at 1.5-A resolution. In addition, two closed ligand-bound structures of the same protein are presented, a phenylalanine-bound form at 1.8 A and a leucine-bound structure at a nominal resolution of 2.4 A. These structures show the basis of this protein's ligand specificity, as well as illustrating the conformational changes that are associated with ligand binding. Comparison with earlier structures provides further information about solution conformations, as well as the different specificity of the closely related leucine/isoleucine/valine-binding protein.


  • Organizational Affiliation
    • Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, S-751 24 Uppsala, Sweden.

Macromolecule Content 

  • Total Structure Weight: 148.84 kDa 
  • Atom Count: 10,633 
  • Modeled Residue Count: 1,384 
  • Deposited Residue Count: 1,384 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LEUCINE-SPECIFIC BINDING PROTEIN
A, B, C, D
346Escherichia coliMutation(s): 0 
UniProt
Find proteins for P04816 (Escherichia coli (strain K12))
Explore P04816 
Go to UniProtKB:  P04816
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04816
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.252 (Depositor), 0.301 (DCC) 
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.421α = 112.79
b = 70.14β = 93.23
c = 79.902γ = 90.97
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.5: 2024-11-13
    Changes: Structure summary