5VQH

Crystal structure of the extended Tudor domain from BmPAPI in complex with sDMA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural studies of the Tudor domain from the Bombyx homolog of Drosophila PAPI: Implication to piRNA biogenesis

Hubbard, P.A.Pan, X.Ohtaki, A.McNally, R.Honda, S.Kirino, Y.Murali, R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tudor and KH domain-containing protein homolog
A, B
237Bombyx moriMutation(s): 0 
Gene Names: PAPI
UniProt
Find proteins for H9JD76 (Bombyx mori)
Explore H9JD76 
Go to UniProtKB:  H9JD76
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH9JD76
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.03α = 90
b = 66.03β = 90
c = 224.48γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106047

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2021-03-10
    Changes: Derived calculations
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description