3AOG | pdb_00003aog

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

PDB DOI: https://doi.org/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 (Depositor), 0.273 (DCC)
R-Value Work:
0.226 (Depositor), 0.224 (DCC)
R-Value Observed:
0.228 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3AOG

This is version 1.1 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.

Macromolecule Content

Total Structure Weight: 580.35 kDa
Atom Count: 40,944
Modeled Residue Count: 5,047
Deposited Residue Count: 5,280
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E 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
UniProt
Find proteins for Q72IC1 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72IC1 Go to UniProtKB: Q72IC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q72IC1
Sequence Annotations 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] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain N [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth K] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth K] mmCIF format, chain W [auth D] mmCIF format, chain WA [auth L] mmCIF format, chain X [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth F] CA [auth F] FA [auth G] GA [auth G] 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		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain QA [auth J] Focus chain R [auth B] Focus chain T [auth C] Focus chain TA [auth K] Focus chain U [auth C] Focus chain UA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain X [auth D] Focus chain XA [auth L] Focus chain Z [auth E]
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] mmCIF format, chain DA [auth F] mmCIF format, chain HA [auth G] mmCIF format, chain NA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth I] mmCIF format, chain RA [auth J] mmCIF format, chain V [auth C] mmCIF format, chain VA [auth K] mmCIF format, chain Y [auth D]	DA [auth F] HA [auth G] NA [auth I] O [auth A] OA [auth I] 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		Interactions Focus chain DA [auth F] Focus chain HA [auth G] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain Y [auth D] Interactions & Density Focus chain DA [auth F] Focus chain HA [auth G] Focus chain NA [auth I] Focus chain O [auth A] Focus chain OA [auth I] Focus chain RA [auth J] Focus chain V [auth C] Focus chain VA [auth K] Focus chain Y [auth D]
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 SA [auth J] SDF format, chain YA [auth L] SDF format, chain S [auth B] MOL2 format, chain EA [auth F] MOL2 format, chain KA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain SA [auth J] MOL2 format, chain YA [auth L] MOL2 format, chain S [auth B] mmCIF format, chain EA [auth F] mmCIF format, chain KA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain SA [auth J] mmCIF format, chain YA [auth L] mmCIF format, chain S [auth B]	EA [auth F] KA [auth H] P [auth A] S [auth B] SA [auth J] 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		Interactions Focus chain EA [auth F] Focus chain KA [auth H] Focus chain P [auth A] Focus chain S [auth B] Focus chain SA [auth J] Focus chain YA [auth L] Interactions & Density Focus chain EA [auth F] Focus chain KA [auth H] Focus chain P [auth A] Focus chain S [auth B] Focus chain SA [auth J] Focus chain YA [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.277 (Depositor), 0.273 (DCC)
R-Value Work: 0.226 (Depositor), 0.224 (DCC)
R-Value Observed: 0.228 (Depositor)

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

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-09-07

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-07
Type: Initial release
Version 1.1: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.