8FW4 | pdb_00008fw4

Crystal structure of the adenosylcobalamin riboswitch holo conformation in absence of ligand

PDB DOI: https://doi.org/10.2210/pdb8FW4/pdb
NAKB: 8FW4

Classification: RNA
Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis
Mutation(s): No

Deposited: 2023-01-20 Released: 2023-07-26
Deposition Author(s): Stagno, J.R., Wang, Y.-X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free:
0.295 (Depositor), 0.294 (DCC)
R-Value Work:
0.263 (Depositor), 0.263 (DCC)
R-Value Observed:
0.264 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8FW4

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

Literature

Crystal structure of cobalamin ribositch in holo conformation without ligand

Ding, J., Stagno, J.R.

(2023) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 68.3 kDa
Atom Count: 3,991
Modeled Residue Count: 185
Deposited Residue Count: 210
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (210-MER)	A [auth Z]	210	Caldanaerobacter subterraneus subsp. tengcongensis
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth Z] MOL2 format, chain B [auth Z] mmCIF format, chain B [auth Z]	B [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth Z] Interactions & Density Focus chain B [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 4.30 Å
R-Value Free: 0.295 (Depositor), 0.294 (DCC)
R-Value Work: 0.263 (Depositor), 0.263 (DCC)
R-Value Observed: 0.264 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.124	α = 90
b = 243.844	β = 90
c = 84.554	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-07-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2023-07-26
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.