7DOV

The crystal structure of zebrafish tumor necrosis factor alpha

PDB DOI: https://doi.org/10.2210/pdb7DOV/pdb

Classification: CYTOKINE
Organism(s): Danio rerio
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-12-17 Released: 2021-12-22
Deposition Author(s): Duan, Y., Xia, C.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.299
R-Value Work: 0.218
R-Value Observed: 0.222

wwPDB Validation 3D Report Full Report

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

Literature

The structure of zebrafish tumour necrosis factor alpha at 2.6 angstrom resolution

Duan, Y., Xia, C.

To be published.

Macromolecule Content

Total Structure Weight: 51.82 kDa
Atom Count: 3,565
Modelled Residue Count: 444
Deposited Residue Count: 465
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphotoxin-alpha	A, B, C	155	Danio rerio	Mutation(s): 0 Gene Names: tnfa
UniProt
Find proteins for Q1L8A5 (Danio rerio) Explore Q1L8A5 Go to UniProtKB: Q1L8A5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1L8A5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.299
R-Value Work: 0.218
R-Value Observed: 0.222
Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.328	α = 90
b = 91.021	β = 90
c = 63.396	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-22

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2021-12-22
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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.