6FAS

Crystal structure of VAL1 B3 domain in complex with cognate DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1.

Sasnauskas, G.Kauneckaite, K.Siksnys, V.

(2018) Nucleic Acids Res. 46: 4316-4324


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
B3 domain-containing transcription repressor VAL1
A, B
119Arabidopsis thalianaGene Names: VAL1 (HSI2)
Find proteins for Q8W4L5 (Arabidopsis thaliana)
Go to UniProtKB:  Q8W4L5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*CP*CP*AP*TP*GP*CP*AP*CP*CP*G)-3')C,E12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*TP*GP*CP*AP*TP*GP*GP*CP*T)-3')D,F12synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.091α = 90.00
b = 86.577β = 94.14
c = 65.160γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-12-17 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Sasnauskas, G.

Funding OrganizationCountryGrant Number
Research Council of LithuaniaLithuaniaMIP-106/2015

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2018-04-25
    Type: Data collection, Database references
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references