1U20

Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29

• PDB DOI: https://doi.org/10.2210/pdb1U20/pdb

• Classification: HYDROLASE
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-07-16 Released: 2005-07-26 
• Deposition Author(s): Scarsdale, J.N., Peculis, B.A., Wright, H.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.254 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Literature

Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29

Scarsdale, J.N., Peculis, B.A., Wright, H.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 48.96 kDa 
• Atom Count: 3,274 
• Modelled Residue Count: 388 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U8 snoRNA-binding protein X29	A, B	212	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for Q6TEC1 (Xenopus laevis) Explore Q6TEC1  Go to UniProtKB:  Q6TEC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.254 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.188	α = 90
b = 82.99	β = 90
c = 111.063	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-07-26 
Deposition Author(s): Scarsdale, J.N., Peculis, B.A., Wright, H.T.

Revision History  

• Version 1.0: 2005-07-26
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations