BMRB Entry 11022

Name: 1H chemical shift assignment for big defensin
Published: 2008-11-11

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PDB ID: 2rng
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR11022
MolProbity Validation Chart

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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:

1H chemical shift assignment for big defensin

Deposition date:

2007-12-26

Original release date:

2008-11-11

Authors:

Kouno, Takahide; Fujitani, Naoki; Osaki, Tsukasa; Kawabata, Shun-ichiro; Nishimura, Shin-ichiro; Mizuguchi, Mineyuki; Aizawa, Tomoyasu; Demura, Makoto; Nitta, Katsutoshi; Kawano, Keiichi

Citation:

Citation: Kouno, Takahide; Fujitani, Naoki; Mizuguchi, Mineyuki; Osaki, Tsukasa; Nishimura, Shin-ichiro; Kawabata, Shun-ichiro; Aizawa, Tomoyasu; Demura, Makoto; Nitta, Katsutoshi; Kawano, Keiichi. "A novel beta-defensin structure: a potential strategy of big defensin for overcoming resistance by Gram-positive bacteria." Biochemistry 47, 10611-10619 (2008).
PubMed: 18785751

Assembly members:

Assembly members:
antimicrobial protein, polymer, 79 residues, 8649.946 Da.

Natural source:

Natural source: Common Name: Tachypleus tridentatus Taxonomy ID: 6853 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Tachypleus tridentatus

Experimental source:

Experimental source: Production method: purified from the natural source

Entity Sequences (FASTA):

Entity Sequences (FASTA):
antimicrobial protein: NPLIPAIYIGATVGPSVWAY LVALVGAAAVTAANIRRASS DNHSCAGNRGWCRSKCFRHE YVDTYYSAVCGRYFCCRSR

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
1H chemical shifts	511

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	antimicrobial protein	1

Entities:

Entity 1, antimicrobial protein 79 residues - 8649.946 Da.

1

ASN

PRO

LEU

ILE

PRO

ALA

ILE

TYR

ILE

GLY

2

ALA

THR

VAL

GLY

PRO

SER

VAL

TRP

ALA

TYR

3

LEU

VAL

ALA

LEU

VAL

GLY

ALA

VAL

4

THR

ALA

ASN

ILE

ARG

ALA

SER

5

ASP

ASN

HIS

SER

CYS

ALA

GLY

ASN

ARG

GLY

6

TRP

CYS

ARG

SER

LYS

CYS

PHE

ARG

HIS

GLU

7

TYR

VAL

ASP

THR

TYR

SER

ALA

VAL

CYS

8

GLY

ARG

TYR

PHE

CYS

ARG

SER

ARG

Samples:

sample_1: big defensin 0.12 mM; acetic acid, [U-100% 2H], 50 mM; sodium chloride 20 mM; DSS 0.05 mM; D2O, [U-100% 2H], 5%; H2O 95%

sample_2: big defensin 0.12 mM; acetic acid, [U-100% 2H], 50 mM; sodium chloride 20 mM; DSS 0.05 mM; D2O, [U-100% 2H], 100%

sample_conditions_1: pH: 3.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D DQF-COSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D DQF-COSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

PIPP, Garrett - data analysis

NMR spectrometers:

Bruker Avance 800 MHz

PDB	2RNG
GB	AAB36095
PRF	2108380A 2112271A
SP	P80957
AlphaFold	P80957