3EOP

Crystal Structure of the DUF55 domain of human thymocyte nuclear protein 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry

Yu, F.Song, A.Xu, C.Sun, L.Li, J.Tang, L.Yu, M.Yeates, T.O.Hu, H.He, J.

(2009) Acta Crystallogr.,Sect.D 65: 212-219

  • DOI: 10.1107/S0907444908041474

  • PubMed Abstract: 
  • Human thymocyte nuclear protein 1 contains a unique DUF55 domain consisting of 167 residues (55-221), but its cellular function remains unclear. Crystals of DUF55 belonged to the trigonal space group P3(1), but twinning caused the data to approach ap ...

    Human thymocyte nuclear protein 1 contains a unique DUF55 domain consisting of 167 residues (55-221), but its cellular function remains unclear. Crystals of DUF55 belonged to the trigonal space group P3(1), but twinning caused the data to approach apparent 622 symmetry. Two data sets were collected to 2.3 A resolution. Statistical analysis confirmed that both data sets were partially twinned by tetartohedry. Tetartohedral twin fractions were estimated. After the structure had been determined, only one twofold axis of rotational pseudosymmetry was found in the crystal structure. Using the DALI program, a YTH domain, which is a potential RNA-binding domain from human YTH-domain-containing protein 2, was identified as having the most similar three-dimensional fold to that of DUF55. It is thus implied that DUF55 might be a potential RNA-related domain.


    Organizational Affiliation

    Shanghai Institute of Applied Physics, Chinese Academy of Sciences, People's Republic of China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymocyte nuclear protein 1
A, B
176Homo sapiensMutation(s): 0 
Gene Names: THYN1 (THY28)
Find proteins for Q9P016 (Homo sapiens)
Go to Gene View: THYN1
Go to UniProtKB:  Q9P016
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 51.258α = 90.00
b = 51.258β = 90.00
c = 122.400γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
CNSrefinement
MAR345dtbdata collection
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance