8PRG

The structure of nvBagel6

PDB DOI: https://doi.org/10.2210/pdb8PRG/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Dictyoglomus thermophilum H-6-12
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2023-07-12 Released: 2024-07-24
Deposition Author(s): Vandebroek, L., Voet, A.R.D., Lee, X.Y.
Funding Organization(s): Research Foundation - Flanders (FWO)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

The structure of v13Bagel2

Vandebroek, L., Voet, A.R.D., Lee, X.Y.

To be published.

Macromolecule Content

Total Structure Weight: 9.05 kDa
Atom Count: 623
Modelled Residue Count: 80
Deposited Residue Count: 84
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell surface protein	A	84	Dictyoglomus thermophilum H-6-12	Mutation(s): 0 Gene Names: DICTH_0179
UniProt
Find proteins for B5YBJ6 (Dictyoglomus thermophilum (strain ATCC 35947 / DSM 3960 / H-6-12)) Explore B5YBJ6 Go to UniProtKB: B5YBJ6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B5YBJ6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.250
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.428	α = 90
b = 54.428	β = 90
c = 48.753	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-07-24

Deposition Author(s):

Funding Organization	Location	Grant Number
Research Foundation - Flanders (FWO)	Belgium	1235722N

Revision History (Full details and data files)

Version 1.0: 2024-07-24
Type: Initial release

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.