6FSW | pdb_00006fsw

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), 0.237 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6FSW

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
Modeled Residue Count: 232
Deposited Residue Count: 236
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O29759
Sequence Annotations Expand
Reference Sequence

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), 0.237 (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

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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

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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.