8K76 | pdb_00008k76

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum

PDB DOI: https://doi.org/10.2210/pdb8K76/pdb

Classification: TRANSFERASE
Organism(s): Fusobacterium nucleatum subsp. nucleatum ATCC 25586
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2023-07-26 Released: 2023-08-23
Deposition Author(s): He, S.R., Bai, X., Zhang, J., Zhao, Z.D.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.214 (Depositor), 0.219 (DCC)
R-Value Observed:
0.215 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of S-adenosylmethionine-dependent methyltransferase from Fusobacterium nucleatum

He, S.R., Bai, X.

To be published.

Macromolecule Content

Total Structure Weight: 57.23 kDa
Atom Count: 3,821
Modeled Residue Count: 478
Deposited Residue Count: 498
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine-dependent methyltransferase	A, B	249	Fusobacterium nucleatum subsp. nucleatum ATCC 25586	Mutation(s): 0 Gene Names: FN1919 EC: 2.1.1
UniProt
Find proteins for Q8R6D8 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)) Explore Q8R6D8 Go to UniProtKB: Q8R6D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8R6D8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.214 (Depositor), 0.219 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.981	α = 90
b = 80.629	β = 90
c = 108.49	γ = 90

Software Package:

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

Structure Validation

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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

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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.