Macromolecule Content

Total Structure Weight: 580.35 kDa
Atom Count: 40944
Modelled Residue Count: 5047
Deposited Residue Count: 5280
Unique protein chains: 1

3AOG

Crystal structure of glutamate dehydrogenase (GdhB) from Thermus thermophilus (Glu bound form)

DOI: 10.2210/pdb3AOG/pdb

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

Deposited: 2010-09-28 Released: 2011-09-07
Deposition Author(s): Tomita, T., Kuzuyama, T., Nishiyama, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.277
R-Value Work: 0.226
R-Value Observed: 0.228

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E, F, G, H A, B, C, D, E, F, G, H, I, J, K, L	440	Thermus thermophilus HB27	Mutation(s): 0 Gene Names: TT_C1211 EC: 1.4.1.3
Find proteins for Q72IC1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)) Explore Q72IC1 Go to UniProtKB: Q72IC1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLU Query on GLU Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain MA [auth I] SDF format, chain N [auth A] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain QA [auth J] SDF format, chain R [auth B] SDF format, chain T [auth C] SDF format, chain TA [auth K] SDF format, chain U [auth C] SDF format, chain UA [auth K] SDF format, chain W [auth D] SDF format, chain WA [auth L] SDF format, chain X [auth D] SDF format, chain XA [auth L] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain W [auth D] MOL2 format, chain WA [auth L] MOL2 format, chain X [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain Z [auth E]	AA [auth E] , BA [auth F] , CA [auth F] , FA [auth G] , GA [auth G] , IA [auth H] , JA [auth H] , LA [auth I] , AA [auth E], BA [auth F], CA [auth F], FA [auth G], GA [auth G], IA [auth H], JA [auth H], LA [auth I], M [auth A], MA [auth I], N [auth A], PA [auth J], Q [auth B], QA [auth J], R [auth B], T [auth C], TA [auth K], U [auth C], UA [auth K], W [auth D], WA [auth L], X [auth D], XA [auth L], Z [auth E]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Ligand Interaction
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain DA [auth F] SDF format, chain HA [auth G] SDF format, chain NA [auth I] SDF format, chain O [auth A] SDF format, chain OA [auth I] SDF format, chain RA [auth J] SDF format, chain V [auth C] SDF format, chain VA [auth K] SDF format, chain Y [auth D] MOL2 format, chain DA [auth F] MOL2 format, chain HA [auth G] MOL2 format, chain NA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth I] MOL2 format, chain RA [auth J] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth K] MOL2 format, chain Y [auth D]	DA [auth F] , HA [auth G] , NA [auth I] , O [auth A] , OA [auth I] , RA [auth J] , V [auth C] , VA [auth K] , DA [auth F], HA [auth G], NA [auth I], O [auth A], OA [auth I], RA [auth J], V [auth C], VA [auth K], Y [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
NH4 Query on NH4 Download Ideal Coordinates CCD File SDF format, chain EA [auth F] SDF format, chain KA [auth H] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain SA [auth J] SDF format, chain YA [auth L] MOL2 format, chain EA [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth J] MOL2 format, chain YA [auth L]	EA [auth F], KA [auth H], P [auth A], S [auth B], SA [auth J], YA [auth L]	AMMONIUM ION H₄ N QGZKDVFQNNGYKY-UHFFFAOYSA-O		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.277
R-Value Work: 0.226
R-Value Observed: 0.228
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.733	α = 82.83
b = 106.546	β = 87.18
c = 166.81	γ = 70.6

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-09-28
Released Date: 2011-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.