7EDC | pdb_00007edc

Crystal structure of mutant tRNA [Gm18] methyltransferase TrmH (E107G) in complex with S-adenosyl-L-methionine from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb7EDC/pdb

Classification: TRANSFERASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-03-15 Released: 2022-03-23
Deposition Author(s): Kono, Y., Ito, A., Okamoto, A., Yamagami, R., Hirata, A., Hori, H.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.242 (Depositor), 0.252 (DCC)
R-Value Work:
0.202 (Depositor), 0.210 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 7EDC

Ligand Structure Quality Assessment

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

Literature

Unique substrate specificity of type II tRNA Gm18 methyltransferase from Escherichia coli

Kono, Y., Ito, A., Okamoto, A., Yamagami, R., Hirata, A., Hori, H.

To be published.

Macromolecule Content

Total Structure Weight: 27.97 kDa
Atom Count: 1,927
Modeled Residue Count: 236
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanosine(18)-2'-O)-methyltransferase	A	249	Escherichia coli	Mutation(s): 1 Gene Names: trmH EC: 2.1.1.34
UniProt
Find proteins for P0AGJ2 (Escherichia coli (strain K12)) Explore P0AGJ2 Go to UniProtKB: P0AGJ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AGJ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 (Subject of Investigation/LOI) Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.242 (Depositor), 0.252 (DCC)
R-Value Work: 0.202 (Depositor), 0.210 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.791	α = 90
b = 60.942	β = 122.965
c = 67.906	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
AutoSol	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-03-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18K06088
Japan Society for the Promotion of Science (JSPS)	Japan	20H03211

Revision History (Full details and data files)

Version 1.0: 2022-03-23
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection, Derived calculations

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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.