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), 0.223 (DCC)
R-Value Work:
0.182 (Depositor), 0.186 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.223 (DCC)
R-Value Work: 0.182 (Depositor), 0.186 (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

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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

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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.