8FV0 | pdb_00008fv0

SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine

PDB DOI: https://doi.org/10.2210/pdb8FV0/pdb
Entry: 8FV0 supersedes: 7KY3

Classification: TRANSFERASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-01-18 Released: 2023-04-26
Deposition Author(s): Tsimbalyuk, S., Forwood, J.K.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.268 (Depositor), 0.270 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine

Tsimbalyuk, S., Forwood, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 60.84 kDa
Atom Count: 4,214
Modeled Residue Count: 496
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diamine N-acetyltransferase	A [auth C], B, C [auth A]	168	Staphylococcus aureus	Mutation(s): 0 Gene Names: res
UniProt
Find proteins for U5NVV0 (Staphylococcus aureus) Explore U5NVV0 Go to UniProtKB: U5NVV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	U5NVV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	D [auth C], E [auth A], F [auth A]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth C] Focus chain E [auth A] Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.268 (Depositor), 0.270 (DCC)
R-Value Work: 0.221 (Depositor), 0.220 (DCC)
R-Value Observed: 0.223 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.098	α = 90
b = 119.951	β = 90
c = 145.522	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-26

Deposition Author(s):

This entry supersedes: 7KY3

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-04-26
Type: Initial release
Version 1.1: 2024-05-22
Changes: Data collection

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.