6MD5

Crystal structure of zebrafish Vps26A

• PDB DOI: https://doi.org/10.2210/pdb6MD5/pdb

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


• Deposited: 2018-09-03 Released: 2018-09-26 
• Deposition Author(s): Collins, B.M., Leneva, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Literature

TBA

Collins, B.M., Leneva, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 37.38 kDa 
• Atom Count: 2,550 
• Modelled Residue Count: 273 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vacuolar protein sorting-associated protein 26A	A	319	Danio rerio	Mutation(s): 0  Gene Names: vps26a, zgc:56673
UniProt
Find proteins for Q6TNP8 (Danio rerio) Explore Q6TNP8  Go to UniProtKB:  Q6TNP8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.219 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.85	α = 90
b = 75.48	β = 90
c = 100.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Currently 6MD5 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Collins, B.M., Leneva, N.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description