8OF6 | pdb_00008of6

Structure of YtoQ

PDB DOI: https://doi.org/10.2210/pdb8OF6/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Bacillus subtilis subsp. subtilis str. 168
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-14 Released: 2024-03-27
Deposition Author(s): Garbers, T.B., Neumann, P., Ficner, R.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.227 (Depositor), 0.230 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of YtoQ

Garbers, T.B., Neumann, P., Ficner, R.

To be published.

Macromolecule Content

Total Structure Weight: 306.52 kDa
Atom Count: 19,706
Modeled Residue Count: 2,366
Deposited Residue Count: 2,720
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
YtoQ	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	170	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0 Gene Names: ytoQ, BSU29850
UniProt
Find proteins for O34305 (Bacillus subtilis (strain 168)) Explore O34305 Go to UniProtKB: O34305
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O34305
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth C]	Q [auth B], R [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain Q [auth B] Focus chain R [auth C] Interactions & Density Focus chain Q [auth B] Focus chain R [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.227 (Depositor), 0.230 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.34	α = 90
b = 70.15	β = 98.91
c = 149.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	--

Revision History (Full details and data files)

Version 1.0: 2024-03-27
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.