8K5L | pdb_00008k5l

Structure of tRNA (cmo5U34)-methyltransferase from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb8K5L/pdb

Classification: TRANSFERASE
Organism(s): Fusobacterium nucleatum
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2023-07-22 Released: 2023-08-23
Deposition Author(s): He, S.R., Bai, X.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free:
0.257 (Depositor), 0.260 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of CmoA from Fusobacterium nucleatum

He, S.R., Bai, X.

To be published.

Macromolecule Content

Total Structure Weight: 198.04 kDa
Atom Count: 13,108
Modeled Residue Count: 1,596
Deposited Residue Count: 1,688
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (cmo5U34)-methyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	211	Fusobacterium nucleatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.67 Å
R-Value Free: 0.257 (Depositor), 0.260 (DCC)
R-Value Work: 0.225 (Depositor), 0.230 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.955	α = 90.03
b = 58.98	β = 90.03
c = 139.69	γ = 90.05

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-23

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: 2023-08-23
Type: Initial release

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.