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), 0.268 (DCC)
R-Value Work:
0.221 (Depositor), 0.220 (DCC)
R-Value Observed:
0.223 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.268 (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

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Ligand Structure Quality Assessment

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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

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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.