6MD5 | pdb_00006md5

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.182 (Depositor), 0.180 (DCC)
R-Value Observed:
0.184 (Depositor)

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

TBA

Collins, B.M., Leneva, N.

To be published.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6TNP8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.182 (Depositor), 0.180 (DCC)
R-Value Observed: 0.184 (Depositor)

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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-09-26
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, 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 R01GM157729.