5VQG | pdb_00005vqg

Crystal structure of the extended Tudor domain from BmPAPI

• PDB DOI: https://doi.org/10.2210/pdb5VQG/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-08 Released: 2017-06-14 
• Deposition Author(s): Hubbard, P.A., Pan, X., Ohtaki, A., McNally, R., Honda, S., Kirino, Y., Murali, R.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.95 kDa 
• Atom Count: 1,629 
• Modeled Residue Count: 203 
• Deposited Residue Count: 237 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tudor and KH domain-containing protein homolog	A	237	Bombyx mori	Mutation(s): 0  Gene Names: PAPI
UniProt
Find proteins for H9JD76 (Bombyx mori) Explore H9JD76  Go to UniProtKB:  H9JD76

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.56	α = 90
b = 63.56	β = 90
c = 100.74	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-14 
Deposition Author(s): Hubbard, P.A., Pan, X., Ohtaki, A., McNally, R., Honda, S., Kirino, Y., Murali, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM106047

Revision History  

• 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
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description