8FCI | pdb_00008fci

tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine

PDB DOI: https://doi.org/10.2210/pdb8FCI/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium avium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-12-01 Released: 2023-12-13
Deposition Author(s): Lavallee, T., Mehta, K., Young, A., Cortes, J., Isaacson, B., Brylewski, J., Schlegel, F., Doti, L., Battaile, K., Stojanoff, V., Perez, A., Bolen, R.
Funding Organization(s): Brookhaven National Laboratory (BNL)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.239 (Depositor), 0.230 (DCC)
R-Value Work:
0.219 (Depositor), 0.210 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

tRNA (N1G37) Methyltransferase (TrmD) of Mycobacterium avium complexed with S-Adenosyl homocysteine

Lavallee, T., Mehta, K., Young, A., Cortes, J., Isaacson, B., Brylewski, J., Schlegel, F., Doti, L., Battaile, K., Stojanoff, V., Perez, A., Bolen, R.

To be published.

Macromolecule Content

Total Structure Weight: 58.07 kDa
Atom Count: 3,243
Modeled Residue Count: 394
Deposited Residue Count: 520
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	260	Mycobacterium avium	Mutation(s): 0 Gene Names: trmD, MAP_2974c EC: 2.1.1.228
UniProt
Find proteins for Q73VN9 (Mycolicibacterium paratuberculosis (strain ATCC BAA-968 / K-10)) Explore Q73VN9 Go to UniProtKB: Q73VN9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q73VN9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAH (Subject of Investigation/LOI) Query on SAH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB: 8FCI	Kd: 1.01e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.239 (Depositor), 0.230 (DCC)
R-Value Work: 0.219 (Depositor), 0.210 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.972	α = 90
b = 70.972	β = 90
c = 240.161	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-12-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Brookhaven National Laboratory (BNL)	United States	DE-SC0012704

Revision History (Full details and data files)

Version 1.0: 2023-12-13
Type: Initial release

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.