3DOJ | pdb_00003doj

Structure of Glyoxylate reductase 1 from Arabidopsis (AtGLYR1)

• PDB DOI: https://doi.org/10.2210/pdb3DOJ/pdb

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


• Deposited: 2008-07-04 Released: 2009-07-07 
• Deposition Author(s): Jorgensen, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Cytosolic NADPH-dependent Glyoxylate Reductase from Arabidopsis: Crystal Structure and Kinetic Characterization of Active Site Mutants

Hoover, G., Jorgensen, R., Merrill, A.R., Shelp, B.J.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 33.06 kDa 
• Atom Count: 2,292 
• Modeled Residue Count: 292 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dehydrogenase-like protein	A	310	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At3g25530 EC: 1.1.1.79
UniProt
Find proteins for Q9LSV0 (Arabidopsis thaliana) Explore Q9LSV0  Go to UniProtKB:  Q9LSV0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.543	α = 90
b = 156.543	β = 90
c = 75.467	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Jorgensen, R.

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description