8VYD

A novel synthase generates m4(2)C to stabilize the archaeal ribosome

PDB DOI: https://doi.org/10.2210/pdb8VYD/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Thermococcus kodakarensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-02-08 Released: 2024-11-06
Deposition Author(s): Ho, P.S., Santangelo, T.J., Fluke, K.
Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.287
R-Value Work: 0.238
R-Value Observed: 0.240

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

A novel synthase generates m4(2)C to stabilize the archaeal ribosome

Fluke, K., Dai, N., Fuchs, R.T., Ho, P.S., Febvre, H.P., Talbott, V., Wolf, E.J., Tsai, Y.-L., Elkins, L., Schiltz, J., Czarny, R., Robb, B., Correa Jr, I.R., Santangelo, T.J.

To be published.

Macromolecule Content

Total Structure Weight: 66.03 kDa
Atom Count: 4,489
Modelled Residue Count: 530
Deposited Residue Count: 580
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SAM-dependent methyltransferase, UPF0020 family	A, B	290	Thermococcus kodakarensis	Mutation(s): 0 Gene Names: TK2045
UniProt
Find proteins for Q5JDR0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDR0 Go to UniProtKB: Q5JDR0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5JDR0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.287
R-Value Work: 0.238
R-Value Observed: 0.240
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.67	α = 90
b = 97.28	β = 99.642
c = 89.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-06

Deposition Author(s):

Ho, P.S.

Santangelo, T.J.

Fluke, K.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2022065
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM143963
National Science Foundation (NSF, United States)	United States	2124202
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM132057

Revision History (Full details and data files)

Version 1.0: 2024-11-06
Type: Initial release

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8VYD

A novel synthase generates m4(2)C to stabilize the archaeal ribosome

A novel synthase generates m4(2)C to stabilize the archaeal ribosome

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)