6AC4 | pdb_00006ac4

Rat Xanthine oxidoreductase, D428N variant

• PDB DOI: https://doi.org/10.2210/pdb6AC4/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2018-07-25 Released: 2019-08-28 
• Deposition Author(s): Okamoto, K., Kawaguchi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Rat Xanthine oxidoreductase, D428A variant, NAD bound form

Okamoto, K., Kawaguchi, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 295.1 kDa 
• Atom Count: 21,692 
• Modeled Residue Count: 2,589 
• Deposited Residue Count: 2,662 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthine dehydrogenase/oxidase	A, B	1,331	Rattus norvegicus	Mutation(s): 1  Gene Names: Xdh EC: 1.17.1.4 (PDB Primary Data), 1.17.3.2 (PDB Primary Data)
UniProt
Find proteins for P22985 (Rattus norvegicus) Explore P22985  Go to UniProtKB:  P22985

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], H [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FES	D [auth A], E [auth A], F [auth B], G [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.296	α = 90
b = 138.648	β = 90
c = 221.865	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Okamoto, K., Kawaguchi, Y.

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Funding Organization	Location	Grant Number
	Japan	15H04702

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description