1VJI | pdb_00001vji

Gene Product of At1g76680 from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb1VJI/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-24 Released: 2004-03-16 
• Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Johnson, K.A., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q3R

Literature

X-ray structure of Arabidopsis At1g77680, 12-oxophytodienoate reductase isoform 1.

Fox, B.G., Malone, T.E., Johnson, K.A., Madson, S.E., Aceti, D., Bingman, C.A., Blommel, P.G., Buchan, B., Burns, B., Cao, J., Cornilescu, C.C., Doreleijers, J., Ellefson, J., Frederick, R., Geetha, H., Hruby, D., Jeon, W.B., Kimball, T., Kunert, J., Markley, J.L., Newman, C., Olson, A., Peterson, F.C., Phillips, G.N., Primm, J., Ramirez, B., Rosenberg, N.S., Runnels, M., Seder, K., Shaw, J., Smith, D.W., Sreenath, H., Song, J., Sussman, M.R., Thao, S., Troestler, D., Tyler, E., Tyler, R., Ulrich, E., Vinarov, D., Vojtik, F., Volkman, B.F., Wesenberg, G., Wrobel, R.L., Zhang, J., Zhao, Q., Zolnai, Z.

(2005) Proteins 61: 206-208

• PubMed: 16080145 
• DOI: https://doi.org/10.1002/prot.20533
• Primary Citation of Related Structures:  
  1VJI

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Organizational Affiliation: 
• University of Wisconsin Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, 53706, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.67 kDa 
• Atom Count: 2,886 
• Modeled Residue Count: 351 
• Deposited Residue Count: 372 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
12-oxophytodienoate reductase (OPR1)	A	372	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At1g76680 EC: 1.3.1.42
UniProt
Find proteins for Q8LAH7 (Arabidopsis thaliana) Explore Q8LAH7  Go to UniProtKB:  Q8LAH7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.293 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.688	α = 90
b = 88.066	β = 90
c = 149.334	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-16 
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Johnson, K.A., Bingman, C.A., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2004-03-16
  Type: Initial release
  
• Version 1.1: 2008-02-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2016-04-06
  Changes: Database references
• Version 1.4: 2017-10-04
  Changes: Refinement description
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Derived calculations