1YDH

X-ray structure of a lysine decarboxylase-like protein from arabidopsis thaliana gene at5g11950

• PDB DOI: https://doi.org/10.2210/pdb1YDH/pdb

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


• Deposited: 2004-12-23 Released: 2005-01-11 
• Deposition Author(s): Wesenberg, G.E., 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: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q4D

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: 48.79 kDa 
• Atom Count: 3,135 
• Modelled Residue Count: 365 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
At5g11950	A, B	216	Arabidopsis thaliana	Mutation(s): 9  Gene Names: AT5G11950
UniProt
Find proteins for Q84MC2 (Arabidopsis thaliana) Explore Q84MC2  Go to UniProtKB:  Q84MC2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	D [auth A], E [auth A], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	C [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-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: 2.15 Å
• R-Value Free: 0.213 
• R-Value Work: 0.159 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.589	α = 90
b = 80.427	β = 102.97
c = 50.709	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-11 
Deposition Author(s): Wesenberg, G.E., Phillips Jr., G.N., Bitto, E., Bingman, C.A., Allard, S.T.M., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2005-01-11
  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: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary