5Z9X

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure of Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with a single-stranded RNA substrate

Chen, J.Liu, L.You, C.Gu, J.Ruan, W.Zhang, L.Cao, C.Gan, J.Huang, Y.Chen, X.Ma, J.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small RNA degrading nuclease 1
A
409Arabidopsis thalianaMutation(s): 0 
Gene Names: SDN1
EC: 3.1.-.-
Find proteins for A3KPE8 (Arabidopsis thaliana)
Go to UniProtKB:  A3KPE8
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3')R10Arabidopsis thaliana
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.252 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.993α = 90.00
b = 87.993β = 90.00
c = 178.639γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Science Foundation of ChinaChinaNSFC 31230041

Revision History 

  • Version 1.0: 2018-06-27
    Type: Initial release