8J4G | pdb_00008j4g

Crystal structure of 11JD mutant-I62N

PDB DOI: https://doi.org/10.2210/pdb8J4G/pdb

Classification: IMMUNE SYSTEM
Organism(s): Anas platyrhynchos, unidentified influenza virus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG, synthetic construct
Mutation(s): Yes

Deposited: 2023-04-19 Released: 2024-04-24
Deposition Author(s): Tang, Z., Zhang, N.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free:
0.258 (Depositor), 0.261 (DCC)
R-Value Work:
0.190 (Depositor), 0.196 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structure of duck MHC 11JD mutant-I62N

Tang, Z., Zhang, N.

To be published.

Macromolecule Content

Total Structure Weight: 88.93 kDa
Atom Count: 6,379
Modeled Residue Count: 758
Deposited Residue Count: 766
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D	271	Anas platyrhynchos	Mutation(s): 1 Gene Names: Anpl-UAA
UniProt
Find proteins for A0A1L5SLS9 (Anas platyrhynchos) Explore A0A1L5SLS9 Go to UniProtKB: A0A1L5SLS9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1L5SLS9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	103	Anas platyrhynchos	Mutation(s): 0 Gene Names: b2m
UniProt
Find proteins for A0A8B9ZF11 (Anas platyrhynchos) Explore A0A8B9ZF11 Go to UniProtKB: A0A8B9ZF11
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8B9ZF11
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide of AIV	C, F	9	unidentified influenza virus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.258 (Depositor), 0.261 (DCC)
R-Value Work: 0.190 (Depositor), 0.196 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.605	α = 90
b = 91.866	β = 90
c = 117.814	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-04-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32172871

Revision History (Full details and data files)

Version 1.0: 2024-04-24
Type: Initial release
Version 1.1: 2024-11-06
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.