2OIG

Crystal structure of RS21-C6 core segment and dm5CTP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of RS21-C6, Involved in Nucleoside Triphosphate Pyrophosphohydrolysis

Wu, B.Liu, Y.Zhao, Q.Liao, S.Zhang, J.Bartlam, M.Chen, W.Rao, Z.

(2007) J.Mol.Biol. 367: 1405-1412

  • DOI: 10.1016/j.jmb.2007.01.057
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RS21-C6, which is highly expressed in all vertebrate genomes and green plants, is proposed to have nucleoside triphosphate pyrophosphohydrolase activity. Here, we report the crystal structures of the core fragment of RS21-C6, named RSCUT, and the com ...

    RS21-C6, which is highly expressed in all vertebrate genomes and green plants, is proposed to have nucleoside triphosphate pyrophosphohydrolase activity. Here, we report the crystal structures of the core fragment of RS21-C6, named RSCUT, and the complex with the substrate 5-methyl dCTP. The refined structure of RSCUT consists mainly of alpha-helices and shows formation of a tightly associated tetramer. On the basis of the structure of the RSCUT-m5dCTP complex and the results of pyrophosphatase activity assays, several key residues involved in the substrate binding of RS21-C6 have been identified. Tetramer formation is shown to be required for substrate binding.


    Organizational Affiliation

    Tsinghua-IBP-Nankai Joint Research Group for Structural Biology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RS21-C6
A, B, C, D
111Mus musculusMutation(s): 0 
Gene Names: Dctpp1 (Tdrg-TL1)
EC: 3.6.1.12
Find proteins for Q9QY93 (Mus musculus)
Go to UniProtKB:  Q9QY93
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
523
Query on 523

Download SDF File 
Download CCD File 
B, D
2'-DEOXY-5-METHYLCYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)
5-METHYL-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE
C10 H19 N3 O13 P3
VSWHQKSDLZFLRY-XLPZGREQSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.188α = 90.00
b = 81.883β = 90.00
c = 87.123γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
MAR345data collection
CNSphasing
HKL-2000data scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-03-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description