1YDH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.152 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
At5g11950
A, B
216Arabidopsis thalianaMutation(s): 0 
Gene Names: LOG8
EC: 3.2.2.n1
Find proteins for Q84MC2 (Arabidopsis thaliana)
Go to UniProtKB:  Q84MC2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.152 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.159 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.589α = 90.00
b = 80.427β = 102.97
c = 50.709γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
RESOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description