3AN1 | pdb_00003an1

Crystal structure of rat D428A mutant, urate bound form

• PDB DOI: https://doi.org/10.2210/pdb3AN1/pdb

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


• Deposited: 2010-08-27 Released: 2010-12-01 
• Deposition Author(s): Okamoto, K., Kawaguchi, Y., Eger, B.T., Pai, E.F., Nishino, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal Structures of Urate Bound Form of Xanthine Oxidoreductase: Substrate Orientation and Structure of the Key Reaction Intermediate

Okamoto, K., Kawaguchi, Y., Eger, B.T., Pai, E.F., Nishino, T.

(2010) J Am Chem Soc 132: 17080-17083

• PubMed: 21077683 
• DOI: https://doi.org/10.1021/ja1077574
• Primary Citation Related Structures: 
  3AMZ, 3AN1


• PubMed Abstract: 
  

  Two contradictory models have been proposed for the binding mode of the substrate xanthine to and its activation mechanism by xanthine oxidoreductase. In an effort to distinguish between the two models, we determined the crystal structures of the urate complexes of the demolybdo-form of the D428A mutant of rat xanthine oxidoreductase at 1.7 Å and of the reduced bovine milk enzyme at 2.1 Å, the latter representing a reaction intermediate. The results clearly indicate the catalytically relevant binding mode of the substrate xanthine.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Nippon Medical School, 1-1-5 Sendagi, Bunkyou-ku, Tokyo 113-8602, Japan.

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)

Macromolecule Content 

• Total Structure Weight: 295.82 kDa 
• Atom Count: 22,752 
• Modeled Residue Count: 2,591 
• 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  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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	G [auth A], N [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
FES	C [auth A], D [auth A], K [auth B], L [auth B]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N
URC	H [auth A], O [auth B]	URIC ACID C5 H4 N4 O3 LEHOTFFKMJEONL-UHFFFAOYSA-N
GOL	J [auth A], Q [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BCT	I [auth A], P [auth B]	BICARBONATE ION C H O3 BVKZGUZCCUSVTD-UHFFFAOYSA-M
CA	E [auth A], F [auth A], M [auth B], R [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.198 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.536	α = 90
b = 138.242	β = 90
c = 222.473	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-01 
Deposition Author(s): Okamoto, K., Kawaguchi, Y., Eger, B.T., Pai, E.F., Nishino, T.

Revision History  

• Version 1.0: 2010-12-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description