3WOV | pdb_00003wov

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 (Depositor), 0.267 (DCC)
R-Value Work:
0.228 (Depositor), 0.234 (DCC)
R-Value Observed:
0.232 (Depositor)

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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
Modeled Residue Count: 457
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.266 (Depositor), 0.267 (DCC)
R-Value Work: 0.228 (Depositor), 0.234 (DCC)
R-Value Observed: 0.232 (Depositor)

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

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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

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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.