1XJ5

X-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 2Q41


Literature

X-RAY STRUCTURE OF SPERMIDINE SYNTHASE FROM ARABIDOPSIS THALIANA GENE AT1G23820

Center for Eukaryotic Structural Genomics

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spermidine synthase 1
A, B, C, D
334Arabidopsis thalianaMutation(s): 8 
Gene Names: AT1G23820
EC: 2.5.1.16
UniProt
Find proteins for Q9ZUB3 (Arabidopsis thaliana)
Explore Q9ZUB3 
Go to UniProtKB:  Q9ZUB3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZUB3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.814α = 90
b = 95.207β = 104.96
c = 89.164γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVEphasing
MOLREPphasing
CNSrefinement
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-02-01
    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
  • Version 1.6: 2024-10-30
    Changes: Structure summary