1U20 | pdb_00001u20

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.254 (Depositor)
R-Value Work:
0.204 (Depositor), 0.211 (DCC)
R-Value Observed:
0.209 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 1U20

This is version 1.3 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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
U8 snoRNA-binding protein X29	A, B	212	Xenopus laevis	Mutation(s): 0 EC: 3.6.1.62 (UniProt), 3.6.1.64 (UniProt)
UniProt
Find proteins for Q6TEC1 (Xenopus laevis) Explore Q6TEC1 Go to UniProtKB: Q6TEC1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6TEC1
Sequence Annotations 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] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.254 (Depositor)
R-Value Work: 0.204 (Depositor), 0.211 (DCC)
R-Value Observed: 0.209 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

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
Version 1.3: 2024-02-14
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.