Macromolecule Content

Total Structure Weight: 48.96 kDa
Atom Count: 3274
Modelled Residue Count: 388
Deposited Residue Count: 424
Unique protein chains: 1

1U20

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

DOI: 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.

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U8 snoRNA-binding protein X29	A, B	212	Xenopus laevis	Mutation(s): 0 Gene Names: nudt16 EC: 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
Find proteins for Q6TEC1 (Xenopus laevis) Explore Q6TEC1 Go to UniProtKB: Q6TEC1
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction

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

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2004-07-16
Released Date: 2005-07-26

Deposition Author(s):

Scarsdale, J.N.

Revision History (Full details and data files)

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.