5YS6 | pdb_00005ys6

Structure of the ectodomain of pseudorabies virus glycoproten B

PDB DOI: https://doi.org/10.2210/pdb5YS6/pdb

Classification: VIRAL PROTEIN
Organism(s): Suid alphaherpesvirus 1
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-11-13 Released: 2017-12-27
Deposition Author(s): Hu, X.L., Yang, F.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free:
0.267 (Depositor), 0.265 (DCC)
R-Value Work:
0.227 (Depositor), 0.233 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Two classes of protective antibodies against pseudorabies virus variant glycoprotein B: implications for vaccine design

Li, X.D., Yang, F.L., Hu, X.L.

To be published.

Macromolecule Content

Total Structure Weight: 78.46 kDa
Atom Count: 4,582
Modeled Residue Count: 572
Deposited Residue Count: 702
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PRV glycoproten B	A	702	Suid alphaherpesvirus 1	Mutation(s): 0 Gene Names: gB
UniProt
Find proteins for T2FL65 (Suid herpesvirus 1) Explore T2FL65 Go to UniProtKB: T2FL65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	T2FL65
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.267 (Depositor), 0.265 (DCC)
R-Value Work: 0.227 (Depositor), 0.233 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.288	α = 90
b = 100.288	β = 90
c = 272.918	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-12-27

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2017-12-27
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: 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.