1VM0 | pdb_00001vm0

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G34160

• PDB DOI: https://doi.org/10.2210/pdb1VM0/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-08-24 Released: 2004-08-31 
• Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.221 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q3V

Literature

X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT2G34160

Center for Eukaryotic Structural Genomics

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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 30.06 kDa 
• Atom Count: 1,733 
• Modeled Residue Count: 196 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
unknown protein	A, B	130	Arabidopsis thaliana	Mutation(s): 7  Gene Names: At2g34160
UniProt
Find proteins for O22969 (Arabidopsis thaliana) Explore O22969  Go to UniProtKB:  O22969

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	D [auth A], F [auth B], G [auth B], H [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
K	C [auth A], E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.221 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.785	α = 90
b = 79.079	β = 90
c = 43.73	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-31 
Deposition Author(s): Wesenberg, G.E., Smith, D.W., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2004-08-31
  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: 2021-10-20
  Changes: Advisory, Database references, Derived calculations
• Version 1.5: 2023-12-27
  Changes: Data collection
• Version 1.6: 2024-11-20
  Changes: Structure summary