8HT3

Crystal structure of immunoglobulin new antigen receptor variable domain from Okamejei kenojei

PDB DOI: https://doi.org/10.2210/pdb8HT3/pdb

Classification: IMMUNE SYSTEM
Organism(s): Okamejei kenojei
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-20 Released: 2023-07-05
Deposition Author(s): Wen, J., Li, P., Bi, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.195
R-Value Observed: 0.201

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Identification and characterization of IgNAR and VNAR repertoire from the ocellate spot skate (Okamejei kenojei)

Wen, J., Gong, J., Li, P., Deng, P., Sun, M., Wu, Y., Tian, C., Wang, H., Bi, Y.

(2023) Front Mar Sci 10: 1183744

DOI: https://doi.org/10.3389/fmars.2023.1183744

Macromolecule Content

Total Structure Weight: 11.53 kDa
Atom Count: 863
Modelled Residue Count: 104
Deposited Residue Count: 104
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
New Antigen Receptor variable domain	A	104	Okamejei kenojei	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.253
R-Value Work: 0.195
R-Value Observed: 0.201
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.901	α = 90
b = 72.213	β = 90
c = 70.139	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CrysalisPro	data reduction
XDS	data scaling
MrBUMP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	41876168

Revision History (Full details and data files)

Version 1.0: 2023-07-05
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references

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 R01GM133198.