4J5T

Crystal structure of Processing alpha-Glucosidase I

PDB DOI: https://doi.org/10.2210/pdb4J5T/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2013-02-09 Released: 2013-04-03
Deposition Author(s): Barker, M.K., Rose, D.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.235
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Specificity of processing alpha-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies.

Barker, M.K., Rose, D.R.

(2013) J Biol Chem 288: 13563-13574

PubMed: 23536181 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.M113.460436
Primary Citation of Related Structures:
4J5T

PubMed Abstract:
The enzyme “GluI” is key to the synthesis of critical glycoproteins in the cell.

Organizational Affiliation

Department of Medical Biophysics, University of Toronto, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, Ontario M5G 2M9, Canada. megan.barker@utoronto.ca

Macromolecule Content

Total Structure Weight: 95.13 kDa
Atom Count: 6,838
Modelled Residue Count: 788
Deposited Residue Count: 811
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-oligosaccharide glucosidase	A	811	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: CWH41, GLS1, YGL027C EC: 3.2.1.106
UniProt
Find proteins for P53008 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53008 Go to UniProtKB: P53008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P53008
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation	Interactions Focus chain B Focus chain C Interactions & Density Focus chain B Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.04 Å
R-Value Free: 0.235
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.8	α = 90
b = 101.8	β = 90
c = 103.3	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-04-03

Deposition Author(s):

Barker, M.K.

Rose, D.R.

Revision History (Full details and data files)

Version 1.0: 2013-04-03
Type: Initial release
Version 1.1: 2013-06-19
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary