7KFF | pdb_00007kff

Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH

PDB DOI: https://doi.org/10.2210/pdb7KFF/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-10-13 Released: 2020-10-28
Deposition Author(s): Michalska, K., Tanase, L., Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free:
0.154 (Depositor), 0.153 (DCC)
R-Value Work:
0.131 (Depositor), 0.132 (DCC)
R-Value Observed:
0.132 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

Crystal structure of TrmD tRNA (guanine-N1)-methyltransferase from Corynebacterium diphtheriae in complex with SAH

Michalska, K., Tanase, L., Maltseva, N., Kim, Y., Endres, M., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 35.26 kDa
Atom Count: 2,259
Modeled Residue Count: 249
Deposited Residue Count: 308
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	308	Corynebacterium diphtheriae	Mutation(s): 0 Gene Names: trmD, BT093_03755, CIP107518_01276 EC: 2.1.1.228
UniProt
Find proteins for Q6NGI5 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NGI5 Go to UniProtKB: Q6NGI5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6NGI5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT 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]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.154 (Depositor), 0.153 (DCC)
R-Value Work: 0.131 (Depositor), 0.132 (DCC)
R-Value Observed: 0.132 (Depositor)

Diffraction Data:

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.619	α = 90
b = 83.619	β = 90
c = 79.418	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-10-28

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History (Full details and data files)

Version 1.0: 2020-10-28
Type: Initial release
Version 2.0: 2024-10-23
Changes: Atomic model, Data collection, Database references, Structure summary