8PRM | pdb_00008prm

The structure of nvBagel2 binding the P8W48O184 polyoxometalate

PDB DOI: https://doi.org/10.2210/pdb8PRM/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: 2.20 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.199 (Depositor), 0.190 (DCC)
R-Value Observed:
0.202 (Depositor)

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: 48.22 kDa
Atom Count: 2,656
Modeled Residue Count: 316
Deposited Residue Count: 336
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, B, C, D	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IR0 (Subject of Investigation/LOI) Query on IR0 Download Ideal Coordinates CCD File SDF format, chain E [auth D] MOL2 format, chain E [auth D] mmCIF format, chain E [auth D]	E [auth D]	P8W48O184 polyoxometalate O₁₈₄ P₈ W₄₈ NPCCKDHTTLWWGE-UHFFFAOYSA-A		Interactions Focus chain E [auth D] Interactions & Density Focus chain E [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.199 (Depositor), 0.190 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.54	α = 90
b = 79.818	β = 90
c = 123.439	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
xia2	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.