8GXD | pdb_00008gxd

L-LEUCINE DEHYDROGENASE FROM EXIGUOBACTERIUM SIBIRICUM

• PDB DOI: https://doi.org/10.2210/pdb8GXD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Exiguobacterium artemiae 255-15
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-19 Released: 2023-04-26 
• Deposition Author(s): Mu, X., Nie, Y., Wu, T., Wang, Y., Zhang, N., Yin, D., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Reshaping Substrate-Binding Pocket of Leucine Dehydrogenase for Bidirectionally Accessing Structurally Diverse Substrates

Wu, T., Wang, Y., Zhang, N., Yin, D., Xu, Y., Nie, Y., Mu, X.

(2023) ACS Catal 13: 158-168

• DOI: https://doi.org/10.1021/acscatal.2c04735

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.04 kDa 
• Atom Count: 2,839 
• Modeled Residue Count: 366 
• Deposited Residue Count: 374 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glu/Leu/Phe/Val dehydrogenase	A	374	Exiguobacterium artemiae 255-15	Mutation(s): 0  Gene Names: Exig_0916 EC: 1.4.1.9
UniProt
Find proteins for B1YLR3 (Exiguobacterium sibiricum (strain DSM 17290 / CCUG 55495 / CIP 109462 / JCM 13490 / 255-15)) Explore B1YLR3  Go to UniProtKB:  B1YLR3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.02 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.99	α = 90
b = 152.99	β = 90
c = 132.02	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-26 
Deposition Author(s): Mu, X., Nie, Y., Wu, T., Wang, Y., Zhang, N., Yin, D., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21336009
National Natural Science Foundation of China (NSFC)	China	21176103

Revision History  

• Version 1.0: 2023-04-26
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Refinement description