7REZ | pdb_00007rez

MYCOBACTERIUM ABSCESSUS TRNA METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE

PDB DOI: https://doi.org/10.2210/pdb7REZ/pdb

Classification: TRANSFERASE
Organism(s): Mycobacteroides abscessus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-07-13 Released: 2023-01-18
Deposition Author(s): Prucha, G.R., Ismail, M., Suske, A., Das, B., Oz, M., Perez, A., Bolen, R., Jayaraman, S., Stojanoff, V., Halloran, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States), Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.216 (Depositor), 0.222 (DCC)
R-Value Work:
0.186 (Depositor)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of divalent Mg+2 dependent Mycobacterium abscessus tRNA (m1 G37) Methyltransferase (TrmD)

Prucha, G.R., Ismail, M., Suske, A., Perez, A., Bolen, R., Jayaraman, S., Stojanoff, V., Halloran, J.

To be published.

Macromolecule Content

Total Structure Weight: 51.7 kDa
Atom Count: 3,788
Modeled Residue Count: 430
Deposited Residue Count: 466
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	233	Mycobacteroides abscessus	Mutation(s): 0 Gene Names: trmD, SAMEA2161603_03547, SAMEA2275821_02238, SAMEA2275847_06627 EC: 2.1.1.228

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 D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.216 (Depositor), 0.222 (DCC)
R-Value Work: 0.186 (Depositor)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.242	α = 90
b = 79.094	β = 90
c = 86.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
ADDREF	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-18

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM133893
Department of Energy (DOE, United States)	United States	DE-SC0012704
Department of Energy (DOE, United States)	United States	KP1605010
Other private	United States	--