1VR3

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.06 Å
R-Value Free: 0.195
R-Value Work: 0.162
R-Value Observed: 0.164

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.20947
Primary Citation of Related Structures:
1VR3

Organizational Affiliation

The Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99JT9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	C [auth A]	Unknown ligand VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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
R-Value Work: 0.162
R-Value Observed: 0.164
Space Group: P 4₁ 2₁ 2
Diffraction Data: https://doi.org/10.18430/M31VR3

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2005-02-15

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.