8DUR | pdb_00008dur

Crystal structure of apo protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri

PDB DOI: https://doi.org/10.2210/pdb8DUR/pdb

Classification: TRANSFERASE
Organism(s): Naegleria fowleri
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-07-27 Released: 2022-08-10
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free:
0.223 (Depositor), 0.223 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of apo protein arginine N-methyltransferase 1 (PRMT1) from Naegleria fowleri

Seibold, S., Liu, L., Battaile, K.P., Lovell, S.

To be published.

Macromolecule Content

Total Structure Weight: 82.97 kDa
Atom Count: 5,130
Modeled Residue Count: 634
Deposited Residue Count: 724
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein arginine N-methyltransferase 1 (PRMT1)	A, B	362	Naegleria fowleri	Mutation(s): 0 Gene Names: FDP41_006519 EC: 2.1.1.319
UniProt
Find proteins for A0A6A5BBK9 (Naegleria fowleri) Explore A0A6A5BBK9 Go to UniProtKB: A0A6A5BBK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6A5BBK9
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.97 Å
R-Value Free: 0.223 (Depositor), 0.223 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.197 (Depositor)

Diffraction Data:

Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.501	α = 90
b = 147.708	β = 90
c = 150.2	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-08-10

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700059C
National Institutes of Health/Office of the Director	United States	S10OD030394

Revision History (Full details and data files)

Version 1.0: 2022-08-10
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Refinement description
Version 1.2: 2023-11-22
Changes: Data collection
Version 1.3: 2024-10-30
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.