8ZMU

GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGANDED STATE

PDB DOI: https://doi.org/10.2210/pdb8ZMU/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermococcus profundus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-05-23 Released: 2024-06-05
Deposition Author(s): Wakabayashi, T., Matsui, Y., Masayoshi, M.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Ministry of Education, Culture, Sports, Science and Technology (Japan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.199
R-Value Work: 0.172
R-Value Observed: 0.174

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by cryoEM-sampling metastable conformation in action

Wakabayashi, T., Matsui, Y., Nakasako, M.

To be published.

Macromolecule Content

Total Structure Weight: 285.87 kDa
Atom Count: 20,653
Modelled Residue Count: 2,475
Deposited Residue Count: 2,514
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate dehydrogenase	A, B, C, D, E A, B, C, D, E, F	419	Thermococcus profundus	Mutation(s): 1 Gene Names: gdhA, gdh EC: 1.4.1.3
UniProt
Find proteins for O74024 (Thermococcus profundus) Explore O74024 Go to UniProtKB: O74024
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O74024
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AB [auth D] SDF format, chain BB [auth D] SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EB [auth E] SDF format, chain FA [auth C] SDF format, chain FB [auth E] SDF format, chain G [auth A] SDF format, chain GA [auth C] SDF format, chain GB [auth E] SDF format, chain H [auth A] SDF format, chain HA [auth C] SDF format, chain HB [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth C] SDF format, chain K [auth A] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain M [auth A] SDF format, chain MA [auth C] SDF format, chain MB [auth F] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain NB [auth F] SDF format, chain O [auth A] SDF format, chain OB [auth F] SDF format, chain P [auth A] SDF format, chain PB [auth F] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth D] SDF format, chain X [auth B] SDF format, chain XA [auth D] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] SDF format, chain ZA [auth D] MOL2 format, chain AB [auth D] MOL2 format, chain BB [auth D] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth E] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth E] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain MB [auth F] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain NB [auth F] MOL2 format, chain O [auth A] MOL2 format, chain OB [auth F] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth F] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth D] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth D] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth D]	AB [auth D] BB [auth D] CB [auth E] DB [auth E] EB [auth E] AB [auth D], BB [auth D], CB [auth E], DB [auth E], EB [auth E], FA [auth C], FB [auth E], G [auth A], GA [auth C], GB [auth E], H [auth A], HA [auth C], HB [auth E], I [auth A], IA [auth C], IB [auth E], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], MB [auth F], N [auth A], NA [auth C], NB [auth F], O [auth A], OB [auth F], P [auth A], PB [auth F], T [auth B], U [auth B], V [auth B], W [auth B], WA [auth D], X [auth B], XA [auth D], Y [auth B], YA [auth D], Z [auth B], ZA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PB [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D] Interactions & Density Focus chain AB [auth D] Focus chain BB [auth D] Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain G [auth A] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain H [auth A] Focus chain HA [auth C] Focus chain HB [auth E] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth E] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain MB [auth F] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth F] Focus chain O [auth A] Focus chain OB [auth F] Focus chain P [auth A] Focus chain PB [auth F] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth D] Focus chain X [auth B] Focus chain XA [auth D] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Focus chain ZA [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain KB [auth E] SDF format, chain LB [auth E] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain KB [auth E] MOL2 format, chain LB [auth E] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C]	CA [auth B] DA [auth B] KB [auth E] LB [auth E] RA [auth C] CA [auth B], DA [auth B], KB [auth E], LB [auth E], RA [auth C], S [auth A], SA [auth C], TA [auth C], UA [auth C], VA [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain DA [auth B] Focus chain KB [auth E] Focus chain LB [auth E] Focus chain RA [auth C] Focus chain S [auth A] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain UA [auth C] Focus chain VA [auth C]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain JB [auth E] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain QA [auth C] SDF format, chain R [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain JB [auth E] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth C] MOL2 format, chain R [auth A]	AA [auth B] BA [auth B] JB [auth E] OA [auth C] PA [auth C] AA [auth B], BA [auth B], JB [auth E], OA [auth C], PA [auth C], Q [auth A], QA [auth C], R [auth A]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain JB [auth E] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain JB [auth E] Focus chain OA [auth C] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain R [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EA [auth B] MOL2 format, chain EA [auth B]	EA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth B] Interactions & Density Focus chain EA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.199
R-Value Work: 0.172
R-Value Observed: 0.174
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.355	α = 90
b = 163.248	β = 113.91
c = 132.605	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

Wakabayashi, T.

Matsui, Y.

Masayoshi, M.

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	jp13480214
Japan Society for the Promotion of Science (JSPS)	Japan	jp19204042
Japan Society for the Promotion of Science (JSPS)	Japan	jp22244054
Japan Society for the Promotion of Science (JSPS)	Japan	jp21H01050
Japan Society for the Promotion of Science (JSPS)	Japan	jp26800227
Japan Society for the Promotion of Science (JSPS)	Japan	18J11653
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp15076210
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp20050030
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp22018027
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp23120525
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp25120725
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp15H01647
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	jp17H05891