1VR3 | pdb_00001vr3

Crystal structure of Acireductone dioxygenase (13543033) from Mus musculus at 2.06 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1VR3/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-01-28 Released: 2005-02-15 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.195 (Depositor), 0.208 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Literature

Crystal structure of acireductone dioxygenase (ARD) from Mus musculus at 2.06 angstrom resolution.

Xu, Q., Schwarzenbacher, R., Krishna, S.S., McMullan, D., Agarwalla, S., Quijano, K., Abdubek, P., Ambing, E., Axelrod, H., Biorac, T., Canaves, J.M., Chiu, H.J., Elsliger, M.A., Grittini, C., Grzechnik, S.K., DiDonato, M., Hale, J., Hampton, E., Han, G.W., Haugen, J., Hornsby, M., Jaroszewski, L., Klock, H.E., Knuth, M.W., Koesema, E., Kreusch, A., Kuhn, P., Miller, M.D., Moy, K., Nigoghossian, E., Paulsen, J., Reyes, R., Rife, C., Spraggon, G., Stevens, R.C., van den Bedem, H., Velasquez, J., White, A., Wolf, G., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2006) Proteins 64: 808-813

• PubMed: 16783794 
• DOI: https://doi.org/10.1002/prot.20947
• Primary Citation Related Structures: 
  1VR3

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Organizational Affiliation: 
• The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 23.6 kDa 
• Atom Count: 1,721 
• Modeled Residue Count: 179 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acireductone dioxygenase	A	191	Mus musculus	Mutation(s): 9  EC: 1.13.11 (PDB Primary Data), 1.13.11.54 (UniProt), 1.13.11.53 (UniProt)
UniProt
Find proteins for Q99JT9 (Mus musculus) Explore Q99JT9  Go to UniProtKB:  Q99JT9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
NI	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N
UNL	C [auth A]	Unknown ligand VEQPNABPJHWNSG-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.195 (Depositor), 0.208 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M31VR3

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.136	α = 90
b = 79.136	β = 90
c = 114.128	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
SCALA	data scaling
autoSHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-15 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-02-15
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary