7E3R | pdb_00007e3r

Crystal structure of TrmL from Vibrio vulnificus

PDB DOI: https://doi.org/10.2210/pdb7E3R/pdb

Classification: TRANSFERASE
Organism(s): Vibrio vulnificus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-02-09 Released: 2022-02-16
Deposition Author(s): Kim, J., Son, J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free:
0.242 (Depositor), 0.247 (DCC)
R-Value Work:
0.200 (Depositor), 0.214 (DCC)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of tRNA mehtyltransferase TrmL from Vibrio vulnificus

Kim, J., Son, J.

To be published.

Macromolecule Content

Total Structure Weight: 18.86 kDa
Atom Count: 1,198
Modeled Residue Count: 146
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A	165	Vibrio vulnificus	Mutation(s): 0 Gene Names: trmL, CRN52_04235 EC: 2.1.1.207
UniProt
Find proteins for Q7MGW0 (Vibrio vulnificus (strain YJ016)) Explore Q7MGW0 Go to UniProtKB: Q7MGW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q7MGW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.79 Å
R-Value Free: 0.242 (Depositor), 0.247 (DCC)
R-Value Work: 0.200 (Depositor), 0.214 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.29	α = 90
b = 52.29	β = 90
c = 119.689	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	--

Revision History (Full details and data files)

Version 1.0: 2022-02-16
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

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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.