6P06

Ternary structure of the E52D mutant of ANT-4 with Neomycin and AMPCPP

PDB DOI: https://doi.org/10.2210/pdb6P06/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Bacillus sp. (in: firmicutes)
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4
Mutation(s): Yes

Deposited: 2019-05-16 Released: 2020-01-29
Deposition Author(s): Selvaraj, B., Cuneo, M.J.
Funding Organization(s): National Science Foundation (NSF, United States), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.221 (Depositor), 0.220 (DCC)
R-Value Work:
0.181 (Depositor), 0.180 (DCC)
R-Value Observed:
0.183 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

"Catch and Release": a Variation of the Archetypal Nucleotidyl Transfer 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: 60.64 kDa
Atom Count: 4,447
Modelled Residue Count: 505
Deposited Residue Count: 512
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kanamycin nucleotidyltransferase	A, B	256	Bacillus sp. (in: firmicutes)	Mutation(s): 1 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05057
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 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 C [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain G [auth A] mmCIF format, chain C [auth A] mmCIF format, chain G [auth A]	C [auth A], G [auth A]	NEOMYCIN C₂₃ H₄₆ N₆ O₁₃ PGBHMTALBVVCIT-VCIWKGPPSA-N		Interactions Focus chain C [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain G [auth A]
APC (Subject of Investigation/LOI) Query on APC Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ CAWZRIXWFRFUQB-IOSLPCCCSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B]	E [auth A], F [auth A], H [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.221 (Depositor), 0.220 (DCC)
R-Value Work: 0.181 (Depositor), 0.180 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.71	α = 90
b = 97.95	β = 90
c = 100.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Selvaraj, B.

Cuneo, M.J.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--
Department of Energy (DOE, United States)	United States	--

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2020-05-06
Changes: Database references
Version 1.2: 2020-05-20
Changes: Database references
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations