7E3S | pdb_00007e3s

Crystal structure of TrmL from Shewanella oneidensis

PDB DOI: https://doi.org/10.2210/pdb7E3S/pdb

Classification: TRANSFERASE
Organism(s): Shewanella oneidensis MR-1
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: 2.10 Å
R-Value Free:
0.239 (Depositor), 0.244 (DCC)
R-Value Work:
0.186 (Depositor), 0.197 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7E3S

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

Literature

Crystal structure of TrmL from Shewanella oneidensis

Kim, J., Son, J.

To be published.

Macromolecule Content

Total Structure Weight: 40.77 kDa
Atom Count: 2,341
Modeled Residue Count: 300
Deposited Residue Count: 368
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cytidine(34)-2'-O)-methyltransferase	A, B	184	Shewanella oneidensis MR-1	Mutation(s): 0 Gene Names: trmL, SO_4529 EC: 2.1.1.207
UniProt
Find proteins for Q8E8X2 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E8X2 Go to UniProtKB: Q8E8X2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8E8X2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.239 (Depositor), 0.244 (DCC)
R-Value Work: 0.186 (Depositor), 0.197 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.816	α = 90
b = 77.988	β = 90
c = 101.044	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

View Full Validation Report

View more in-depth experimental data

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.