1US5 | pdb_00001us5

PUTATIVE GLUR0 LIGAND BINDING CORE WITH L-GLUTAMATE

• PDB DOI: https://doi.org/10.2210/pdb1US5/pdb

• Classification: RECEPTOR
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-11-18 Released: 2003-11-19 
• Deposition Author(s): Tahirov, T.H., Inagaki, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

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

• PubMed: 15388932 
• 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.

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

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 33.7 kDa 
• Atom Count: 2,592 
• Modeled Residue Count: 298 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE GLUR0 LIGAND BINDING CORE	A	314	Thermus thermophilus HB8	Mutation(s): 0
UniProt
Find proteins for P83817 (Thermus thermophilus) Explore P83817  Go to UniProtKB:  P83817

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GLU	B [auth A]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.44	α = 90
b = 69.476	β = 90
c = 103.798	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-19 
Deposition Author(s): Tahirov, T.H., Inagaki, E.

Revision History  

• 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: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description