6JV3

Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.851 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine

Fu, T.Liu, L.Yang, Q.L.Wang, Y.Xu, P.Zhang, L.Liu, S.Dai, Q.Ji, Q.Xu, G.L.He, C.Luo, C.Zhang, L.

(2019) Chem Sci --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')A,B,C,D10Homo sapiens
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5HC
Query on 5HC
A, B, C, D
DNA LINKINGC10 H16 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.851 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.907α = 90.00
b = 23.818β = 111.12
c = 85.556γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
PHASERphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-04-15 
  • Released Date: 2019-07-31 
  • Deposition Author(s): Zhang, L., Wang, Y.X.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina21572133
National Natural Science Foundation of ChinaChina21722802

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release