3WOV

Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (PaAglB-L, Q9V250_PYRAB, PAB2202) from Pyrococcus abyssi

PDB DOI: https://doi.org/10.2210/pdb3WOV/pdb

Classification: TRANSFERASE
Organism(s): Pyrococcus abyssi GE5
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-01-05 Released: 2014-01-22
Deposition Author(s): Matsuoka, R., Nyirenda, J., Maita, N., Kohda, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.266
R-Value Work: 0.228
R-Value Observed: 0.232

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of the C-terminal globular domain of oligosaccharyltransferase (PaAglB-L, Q9V250_PYRAB, PAB2202) from Pyrococcus abyssi

Matsuoka, R., Nyirenda, J., Maita, N., Kohda, D.

To be published.

Macromolecule Content

Total Structure Weight: 57.85 kDa
Atom Count: 3,650
Modelled Residue Count: 457
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oligosaccharyl transferase	A	512	Pyrococcus abyssi GE5	Mutation(s): 0 Gene Names: PAB2202, PYRAB02240 EC: 2.4.99.21
UniProt
Find proteins for Q9V250 (Pyrococcus abyssi (strain GE5 / Orsay)) Explore Q9V250 Go to UniProtKB: Q9V250
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9V250
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.266
R-Value Work: 0.228
R-Value Observed: 0.232
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.748	α = 90
b = 70.748	β = 90
c = 204.75	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data collection
PHASER	phasing
PHENIX	refinement
autoPROC	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-01-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-22
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary

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.