6UN8 | pdb_00006un8

Wild type ANT bound to neomycin

PDB DOI: https://doi.org/10.2210/pdb6UN8/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2019-10-11 Released: 2020-05-06
Deposition Author(s): Cuneo, M.J., Selvaraj, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

"Catch and Release": a Variation of the Archetypal NucleotidylTransfer Reaction

Selvaraj, B., Kocaman, S., Trifas, M., Serpersu, E.H., Cuneo, M.J.

(2020) ACS Catal 10: 3548-3555

DOI: https://doi.org/10.1021/acscatal.9b05201

Macromolecule Content

Total Structure Weight: 58.9 kDa
Atom Count: 4,739
Modeled Residue Count: 505
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoglycoside NucleotidylTransferase	A, B	253	Staphylococcus aureus	Mutation(s): 0 Gene Names: knt, kan EC: 2.7.7
UniProt
Find proteins for P05057 (Staphylococcus aureus) Explore P05057 Go to UniProtKB: P05057
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05057
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NMY (Subject of Investigation/LOI) Query on NMY Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	NEOMYCIN C₂₃ H₄₆ N₆ O₁₃ PGBHMTALBVVCIT-VCIWKGPPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.198 (Depositor), 0.199 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.661	α = 90
b = 97.794	β = 90
c = 102.231	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
PDB_EXTRACT	data extraction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2020-05-06

Deposition Author(s):

Cuneo, M.J.

Selvaraj, B.

Revision History (Full details and data files)

Version 1.0: 2020-05-06
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description

6UN8 | pdb_00006un8

Wild type ANT bound to neomycin

Literature

"Catch and Release": a Variation of the Archetypal NucleotidylTransfer Reaction

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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