1US4 | pdb_00001us4

PUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.206 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history. 

Literature

Structure of the Thermus Thermophilus Putative Periplasmic Glutamate/Glutamine-Binding Protein

Takahashi, H., Inagaki, E., Kuroishi, C., Tahirov, T.H.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1846

  • DOI: https://doi.org/10.1107/S0907444904019420
  • Primary Citation Related Structures: 
    1US4, 1US5

  • PubMed Abstract: 

    As part of a structural genomics project, the crystal structure of a 314-amino-acid protein encoded by Thermus thermophilus HB8 gene TT1099 was solved to 1.75 A using the multiple-wavelength anomalous dispersion (MAD) method and a selenomethionine-incorporated protein. The native protein structure was solved to 1.5 A using the molecular-replacement method. Both structures revealed a bound ligand, L-glutamate or L-glutamine, and a fold related to the periplasmic substrate-binding proteins (PSBP). Further comparative structural analysis with other PSBP-fold proteins revealed the conservation of the predicted membrane permease binding surface area and indicated that the T. thermophilus HB8 molecule is most likely to be an L-glutamate and/or an L-glutamine-binding protein related to the cluster 3 periplasmic receptors. However, the geometry of ligand binding is unique to the T. thermophilus HB8 molecule.

    • Organizational Affiliation: 
    • Highthroughput Factory, RIKEN Harima Institute, 1-1-1 Kouto, Mikazuki-cho, Sayo-gun, Hyogo 679-5148, Japan.

Macromolecule Content 

  • Total Structure Weight: 33.93 kDa 
  • Atom Count: 2,508 
  • Modeled Residue Count: 298 
  • Deposited Residue Count: 314 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PUTATIVE GLUR0 LIGAND BINDING CORE314Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P83817 (Thermus thermophilus)
Explore P83817 
Go to UniProtKB:  P83817
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83817
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.206 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.518α = 90
b = 68.092β = 90
c = 81.381γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
ARP/wARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-19
    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: 2017-06-28
    Changes: Refinement description
  • Version 1.4: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2019-05-22
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2024-11-13
    Changes: Data collection, Database references, Structure summary