8RI0 | pdb_00008ri0

Crystal structure of Tm1570 domain from Calditerrivibrio nitroreducens in complex with S-adenosyl-L-methionine

PDB DOI: https://doi.org/10.2210/pdb8RI0/pdb

Classification: TRANSFERASE
Organism(s): Calditerrivibrio nitroreducens DSM 19672
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-12-18 Released: 2024-01-10
Deposition Author(s): Kluza, A., Lewandowska, I., Sulkowska, J.
Funding Organization(s): Polish National Science Centre, European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.206 (Depositor), 0.207 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Are there double knots in proteins? Prediction and in vitro verification based on TrmD-Tm1570 fusion from C. nitroreducens. To be published

Sulkowska, J.

To be published.

Macromolecule Content

Total Structure Weight: 47.73 kDa
Atom Count: 2,727
Modeled Residue Count: 340
Deposited Residue Count: 410
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	205	Calditerrivibrio nitroreducens DSM 19672	Mutation(s): 0 Gene Names: trmD, Calni_2012 EC: 2.1.1.228
UniProt
Find proteins for E4THH1 (Calditerrivibrio nitroreducens (strain DSM 19672 / NBRC 101217 / Yu37-1)) Explore E4THH1 Go to UniProtKB: E4THH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E4THH1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 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 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-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-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: 1.95 Å
R-Value Free: 0.250 (Depositor), 0.250 (DCC)
R-Value Work: 0.206 (Depositor), 0.207 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.85	α = 90
b = 48.09	β = 116.22
c = 79.81	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-01-10

Deposition Author(s):

Lewandowska, I.

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2018/31/B/NZ1/04016
European Union (EU)	European Union	COST EUTOPIA action

Revision History (Full details and data files)

Version 1.0: 2024-01-10
Type: Initial release

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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.