6Q57 | pdb_00006q57

X-ray crystal structure of the tetrahydrofolate riboswitch aptamer bound to 5-deazatetrahydropterin

PDB DOI: https://doi.org/10.2210/pdb6Q57/pdb
NAKB: 6Q57

Classification: RNA
Organism(s): Streptococcus mutans UA159
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2018-12-07 Released: 2019-12-18
Deposition Author(s): Dunstan, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free:
0.248 (Depositor), 0.246 (DCC)
R-Value Work:
0.210 (Depositor), 0.215 (DCC)
R-Value Observed:
0.212 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6Q57

Ligand Structure Quality Assessment

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

Literature

Tetrahydrofolate Riboswitches Provide Distinct Genetic Outputs to Synthetic and Natural Signals.

Vincent, H.A., Leigh, J., Robinson, C.J., Dunstan, M.S., Ferrer Rios, M.G., Micklefield, J.

To be published.

Macromolecule Content

Total Structure Weight: 29.21 kDa
Atom Count: 1,940
Modeled Residue Count: 89
Deposited Residue Count: 89
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
tetrahydrofolate riboswitch aptamer	A	89	Streptococcus mutans UA159
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
T0A Query on T0A Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	5-deazatetrahydropterin C₇ H₁₀ N₄ O PRQFDDYAWVNJMM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.72 Å
R-Value Free: 0.248 (Depositor), 0.246 (DCC)
R-Value Work: 0.210 (Depositor), 0.215 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.863	α = 90
b = 68.697	β = 90
c = 157.309	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-12-18

Deposition Author(s):

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2019-12-18
Type: Initial release
Version 1.1: 2024-05-15
Changes: Data collection, Database references

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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.