5W82 | pdb_00005w82

Crystal structure of Orsay virus delta protein N-terminal fragment (aa 1-101)

PDB DOI: https://doi.org/10.2210/pdb5W82/pdb

Classification: VIRAL PROTEIN
Organism(s): Orsay virus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-06-21 Released: 2018-12-26
Deposition Author(s): Guo, Y.R., Tao, Y.J.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.226 (Depositor), 0.229 (DCC)
R-Value Work:
0.186 (Depositor), 0.189 (DCC)
R-Value Observed:
0.188 (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

To be published

Guo, Y.R., Tao, Y.J.

To be published.

Macromolecule Content

Total Structure Weight: 58.33 kDa
Atom Count: 4,539
Modeled Residue Count: 504
Deposited Residue Count: 515
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein delta	A [auth C], B, C [auth D], D [auth E], E [auth A]	103	Orsay virus	Mutation(s): 0
UniProt
Find proteins for A0ACD6B8I9 (Orsay virus) Explore A0ACD6B8I9 Go to UniProtKB: A0ACD6B8I9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B8I9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.226 (Depositor), 0.229 (DCC)
R-Value Work: 0.186 (Depositor), 0.189 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.746	α = 90
b = 58.22	β = 90
c = 163.235	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2018-12-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI122356

Revision History (Full details and data files)

Version 1.0: 2018-12-26
Type: Initial release
Version 1.1: 2019-12-11
Changes: Author supporting evidence
Version 1.2: 2023-10-04
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.