6CU3 | pdb_00006cu3

Crystal structure of a protein arginine N-methyltransferase from Naegleria fowleri

PDB DOI: https://doi.org/10.2210/pdb6CU3/pdb

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

Deposited: 2018-03-23 Released: 2018-04-04
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.233 (Depositor), 0.236 (DCC)
R-Value Work:
0.190 (Depositor), 0.194 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a protein arginine N-methyltransferase from Naegleria fowleri

Edwards, T.E., Dranow, D.M., Lorimer, D.D., Horanyi, P.S.

To be published.

Macromolecule Content

Total Structure Weight: 233.3 kDa
Atom Count: 14,652
Modeled Residue Count: 1,819
Deposited Residue Count: 2,016
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein arginine N-methyltransferase	A, B, C, D, E A, B, C, D, E, F	336	Naegleria fowleri	Mutation(s): 0 EC: 2.1.1.319
UniProt
Find proteins for A0A384E135 (Naegleria fowleri) Explore A0A384E135 Go to UniProtKB: A0A384E135
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A384E135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain X [auth E] SDF format, chain R [auth E] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain X [auth E] MOL2 format, chain R [auth E] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain X [auth E] mmCIF format, chain R [auth E] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth B], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth C], R [auth E], S [auth E], T [auth E], U [auth E], V [auth E], W [auth E], X [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth E] Focus chain W [auth E] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.233 (Depositor), 0.236 (DCC)
R-Value Work: 0.190 (Depositor), 0.194 (DCC)
R-Value Observed: 0.191 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 249.63	α = 90
b = 101.46	β = 90
c = 105.89	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-04-04

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2018-04-04
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-23
Changes: Structure summary