1VK0

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450

• PDB DOI: https://doi.org/10.2210/pdb1VK0/pdb

• Classification: structural genomics, unknown function
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-04-12 Released: 2004-04-27 
• 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: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q3S

Literature

X-ray Structure of Gene Product from Arabidopsis Thaliana At5g06450

Center for Eukaryotic Structural Genomics

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content

• Total Structure Weight: 139.46 kDa 
• Atom Count: 10,215 
• Modelled Residue Count: 1,200 
• Deposited Residue Count: 1,236 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B, C, D, E, F	206	Arabidopsis thaliana	Mutation(s): 1  Gene Names: At5g06450 EC: 3.1.13.1
UniProt
Find proteins for Q9FNG3 (Arabidopsis thaliana) Explore Q9FNG3  Go to UniProtKB:  Q9FNG3

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.233 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.831	α = 90
b = 120.831	β = 90
c = 185.222	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-04-27 
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: 2004-04-27
  Type: Initial release
  
• Version 1.1: 2008-02-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Structure summary