2A33

X-Ray Structure of a Lysine Decarboxylase-Like Protein from Arabidopsis Thaliana Gene AT2G37210

• PDB DOI: https://doi.org/10.2210/pdb2A33/pdb

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


• Deposited: 2005-06-23 Released: 2005-07-19 
• Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Mccoy, J.G., 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: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4O

Literature

X-ray crystal structures of the conserved hypothetical proteins from Arabidopsis thaliana gene loci At5g11950 and AT2g37210.

Jeon, W.B., Allard, S.T.M., Bingman, C.A., Bitto, E., Han, B.W., Wesenberg, G.E., Phillips Jr., G.N.

(2006) Proteins 65: 1051-1054

• PubMed: 17048257 
• DOI: https://doi.org/10.1002/prot.21166
• Primary Citation of Related Structures:  
  1YDH, 2A33

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Organizational Affiliation: 

Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 48.05 kDa 
• Atom Count: 2,869 
• Modelled Residue Count: 348 
• Deposited Residue Count: 430 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein	A, B	215	Arabidopsis thaliana	Mutation(s): 7  Gene Names: At2g37210
UniProt
Find proteins for Q8L8B8 (Arabidopsis thaliana) Explore Q8L8B8  Go to UniProtKB:  Q8L8B8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.181 
• R-Value Observed: 0.183 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.403	α = 90
b = 66.773	β = 90
c = 98.639	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-19 
Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Mccoy, J.G., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2005-07-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection