6R45 | pdb_00006r45

Crystal structure of eukaryotic O-GlcNAcase HAT-like domain

PDB DOI: https://doi.org/10.2210/pdb6R45/pdb

Classification: TRANSFERASE
Organism(s): Trichoplax adhaerens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-03-21 Released: 2020-04-08
Deposition Author(s): Raimi, O.G., Gorelik, A., Hopkins-Navratilova, I., Aristotelous, T., Ferenbach, A., vanAalten, D.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.240 (Depositor), 0.241 (DCC)
R-Value Work:
0.193 (Depositor), 0.201 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of eukaryotic O-GlcNAcase HAT-like domain

Raimi, O.G., Gorelik, A.

To be published.

Macromolecule Content

Total Structure Weight: 49.79 kDa
Atom Count: 3,578
Modeled Residue Count: 409
Deposited Residue Count: 422
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
O-GlcNAcase	A, B	211	Trichoplax adhaerens	Mutation(s): 0 EC: 3.2.1.169
UniProt
Find proteins for A0A0D5X2Y8 (Trichoplax adhaerens) Explore A0A0D5X2Y8 Go to UniProtKB: A0A0D5X2Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0D5X2Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.240 (Depositor), 0.241 (DCC)
R-Value Work: 0.193 (Depositor), 0.201 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.25	α = 87.52
b = 43.52	β = 85.24
c = 59.84	γ = 87.58

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-08

Deposition Author(s):

Hopkins-Navratilova, I.

Aristotelous, T.

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2020-04-08
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.