8W9S | pdb_00008w9s

NAD-dependent dehydrogenase

• PDB DOI: https://doi.org/10.2210/pdb8W9S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Amycolatopsis mediterranei S699
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-09-05 Released: 2025-03-12 
• Deposition Author(s): Niu, M., Shen, Y.M.
• Funding Organization(s): National Natural Science Foundation of China (NSFC), National Basic Research Program of China (973 Program)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Deciphering the Naphthalenic Ring Formation mechanism in the Biosynthesis of rifamycins

Niu, M., Shen, Y.M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Dihedral - D2  (Explore in 3D)
Pseudo Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 125.11 kDa 
• Atom Count: 9,164 
• Modeled Residue Count: 1,149 
• Deposited Residue Count: 1,196 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-dependent dihydrogenase	A, C	342	Amycolatopsis mediterranei S699	Mutation(s): 0
UniProt
Find proteins for O52541 (Amycolatopsis mediterranei) Explore O52541  Go to UniProtKB:  O52541

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RifT	B, D	256	Amycolatopsis mediterranei S699	Mutation(s): 0  Gene Names: rifT
UniProt
Find proteins for O52542 (Amycolatopsis mediterranei) Explore O52542  Go to UniProtKB:  O52542

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD (Subject of Investigation/LOI)	E [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
US6 (Subject of Investigation/LOI)	F [auth A], G [auth C]	(7E,9S,10S,11R,12R,13R,14R,15R,16S,17S,18E,20Z)-2,4,10,12,14,16-hexahydroxy-3,7,9,11,13,15,17,21-octamethyl-23-azatricyclo[22.3.1.05,27]octacosa-1,3,5(27),7,18,20,24-heptaene-6,22,26,28-tetrone C35 H45 N O10 VFGOUSMZKMNRLA-CVQHHNHTSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.539	α = 90
b = 82.11	β = 99.64
c = 88.555	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PHASER	phasing
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Niu, M., Shen, Y.M.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81530091
National Basic Research Program of China (973 Program)	China	2019YFA0905402

Revision History  

• Version 1.0: 2025-03-12
  Type: Initial release