BMRB Entry 31130

Name: Solution NMR structure of recifin A [Y6F]
Published: 2024-09-18

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PDB ID: 8v2v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31130
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Solution NMR structure of recifin A [Y6F]

Deposition date:

2023-11-23

Original release date:

2024-09-18

Authors:

Payne, C.; Schroeder, C.; Rosengren, K.

Citation:

Citation: Smallwood, Taylor; Krumpe, Lauren; Payne, Colton; Klein, Victoria; O'Keefe, Barry; Clark, Richard; Schroeder, Christina; Rosengren, K Johan. "Picking the tyrosine-lock: chemical synthesis of the tyrosyl-DNA phosphodiesterase I inhibitor recifin A and analogues" Chem. Sci. 15, 13227-13233 (2024).
PubMed: 39183914

Assembly members:

Assembly members:
entity_1, polymer, 41 residues, 4797.343 Da.
entity_PCA, non-polymer, 129.114 Da.

Natural source:

Natural source: Common Name: Axinella sp. 1 TF-2017 Taxonomy ID: 2041915 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Axinella Axinella sp. 1 TF-2017

Experimental source:

Experimental source: Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: EAFCFSDRFCQNYIGSIPDC CFGRGSYSFELQPPPWECYQ C

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	75
15N chemical shifts	17
1H chemical shifts	269

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 41 residues - 4797.343 Da.

1

GLU

ALA

PHE

CYS

PHE

SER

ASP

ARG

PHE

CYS

2

GLN

ASN

TYR

ILE

GLY

SER

ILE

PRO

ASP

CYS

3

CYS

PHE

GLY

ARG

GLY

SER

TYR

SER

PHE

GLU

4

LEU

GLN

PRO

TRP

GLU

CYS

TYR

GLN

5

CYS

Entity 2, unit_2 - C5 H7 N O3 - 129.114 Da.

1

PCA

Samples:

sample_1: recifin A [Y6F] 1 mM

sample_conditions_1: ionic strength: 0 mM; pH: 4.9; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

CARA, Keller and Wuthrich - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS v1.2, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AVANCE III 900 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks