6FSW

Structure of Archaeoglobus fulgidus SBDS protein at 1.9 Angstrom

PDB DOI: https://doi.org/10.2210/pdb6FSW/pdb

Classification: RIBOSOMAL PROTEIN
Organism(s): Archaeoglobus fulgidus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-02-20 Released: 2018-03-21
Deposition Author(s): Mazzorana, M., Foadi, J., Siliqi, D., Sanchez-Puig, N.
Funding Organization(s): CONACyT, Ministero degli Affari Esteri e dalla Cooperazione Internazionale, Diamond Light Source

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.233 (Depositor), 0.240 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Conformational flexibility of proteins involved in ribosome biogenesis: investigations via Small Angle X-ray Scattering (SAXS)

Siliqi, D., Foadi, J., Mazzorana, M., Altamura, D., Mendez Godoy, A., Sanchez Puig, N.

(2018) Crystals (Basel) 8: 109

DOI: https://doi.org/10.3390/cryst8030109

Macromolecule Content

Total Structure Weight: 26.91 kDa
Atom Count: 1,949
Modelled Residue Count: 232
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome maturation protein SDO1-like protein	A	236	Archaeoglobus fulgidus	Mutation(s): 0 Gene Names: XD40_1041, XD48_1723
UniProt
Find proteins for O29759 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O29759 Go to UniProtKB: O29759
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O29759
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.233 (Depositor), 0.240 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.81	α = 75.08
b = 44.52	β = 84.52
c = 54.71	γ = 69.72

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Sanchez-Puig, N.

Funding Organization	Location	Grant Number
CONACyT	Mexico	283909
Ministero degli Affari Esteri e dalla Cooperazione Internazionale	Italy	PGR2014-2017
Diamond Light Source	United Kingdom	MX11690-13

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2024-01-17
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.