BMRB Entry 30767

Name: Solution NMR structure of recifin, a cysteine-rich tyrosyl-DNA Phosphodiesterase I modulatory peptide from the marine sponge Axinella sp.
Published: 2021-02-04

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PDB ID: 6xn9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30767
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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 cysteine-rich tyrosyl-DNA Phosphodiesterase I modulatory peptide from the marine sponge Axinella sp.

Deposition date:

2020-07-02

Original release date:

2021-02-04

Authors:

Schroeder, C.; Rosengren, K.; O'Keefe, B.

Citation:

Citation: Krumpe, Lauren; Wilson, Brice; Marchand, Christophe; Sunassee, Suthananda; Bermingham, Alun; Wang, Wenjie; Price, Edmund; Guszczynski, Tad; Kelley, James; Gustafson, Kirk; Pommier, Yves; Rosengren, K Johan; Schroeder, Christina; O'Keefe, Barry. "Recifin A, Initial Example of the Tyr-Lock Peptide Structural Family, Is a Selective Allosteric Inhibitor of Tyrosyl-DNA Phosphodiesterase I" J. Am. Chem. Soc. 142, 21178-21188 (2020).
PubMed: 33263997

Assembly members:

Assembly members:
entity_1, polymer, 42 residues, 4924.441 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: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: XEAFCYSDRFCQNYIGSIPD CCFGRGSYSFELQPPPWECY QC

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	98
1H chemical shifts	271

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 42 residues - 4924.441 Da.

1

PCA

GLU

ALA

PHE

CYS

TYR

SER

ASP

ARG

PHE

2

CYS

GLN

ASN

TYR

ILE

GLY

SER

ILE

PRO

ASP

3

CYS

PHE

GLY

ARG

GLY

SER

TYR

SER

PHE

4

GLU

LEU

GLN

PRO

TRP

GLU

CYS

TYR

5

GLN

CYS

Samples:

sample_1: recifin 4 mg/mL

sample_2: recifin 4 mg/mL

sample_conditions_1: ionic strength: 0 mM; pH: 4.85; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v3.5, Bruker Biospin - collection, processing

CcpNmr Analysis v2.4.1, CCPN - chemical shift assignment

XEASY, Bartels et al. - data analysis

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

NMR spectrometers:

Bruker AVANCE III 600 MHz