3AOE | pdb_00003aoe

Crystal structure of hetero-hexameric glutamate dehydrogenase from Thermus thermophilus (Leu bound form)

• PDB DOI: https://doi.org/10.2210/pdb3AOE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-27 Released: 2011-09-07 
• Deposition Author(s): Tomita, T., Kuzuyama, T., Nishiyama, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.260 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

An unique allosteric regulation revealed by hetero-hexameric glutamate dehydrogenase from Thermus thermophilus

Tomita, T., Kuzuyama, T., Nishiyama, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 Pseudo Symmetry: Dihedral - D3  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 271.58 kDa 
• Atom Count: 19,355 
• Modeled Residue Count: 2,512 
• Deposited Residue Count: 2,524 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B	424	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: gdhB, TT_C1211 EC: 1.4.1.3
UniProt
Find proteins for Q72IC1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IC1  Go to UniProtKB:  Q72IC1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	C [auth E], D [auth F], E [auth C], F [auth D]	419	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: gdhA, TT_C1212 EC: 1.4.1.3
UniProt
Find proteins for Q72IC0 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IC0  Go to UniProtKB:  Q72IC0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LEU	G [auth A], H [auth B], I [auth E], J [auth F], K [auth C], L [auth D]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.260 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.986	α = 90
b = 146.093	β = 90
c = 158.284	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Tomita, T., Kuzuyama, T., Nishiyama, M.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-03-20
  Changes: Source and taxonomy, Structure summary