7DOV | pdb_00007dov

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

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

Duan, Y., Xia, C.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

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

Macromolecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.299 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

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

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-22 
Deposition Author(s): Duan, Y., Xia, C.

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

Revision History  

• Version 1.0: 2021-12-22
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary