BMRB Entry 50808

Name: Backbone and sidechain 1H, 13C, and 15N Chemical Shift assignments for nanobody Nb23
Published: 2021-06-11

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR50808

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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:

Backbone and sidechain 1H, 13C, and 15N Chemical Shift assignments for nanobody Nb23

Deposition date:

2021-03-08

Original release date:

2021-06-11

Authors:

Percipalle, Mathias; Hunashal, Yamanappa; Esposito, Gennaro

Citation:

Citation: Percipalle, Mathias; Hunashal, Yamanappa; Esposito, Gennaro. "Structure of Nanobody Nb23" Molecules 26, 3567-3567 (2021).

Assembly members:

Assembly members:
entity_1, polymer, 129 residues, Formula weight is not available

Natural source:

Natural source: Common Name: Llama glama Taxonomy ID: 9844 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Llama glama

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET-22b(+)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: QVQLQESGGGLVQAGGSLRL SCAASGRTFSSYAMAWFRQA PGKEREFVARISGVGTNTYY TDSVKGRVTISRDNAKNTVY LQMNSLKPEDTAVYYCAASI YGYYSDTSYYTRLNNYLYWG QGTQVTVSS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	455
15N chemical shifts	121
1H chemical shifts	754

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Nb23	1

Entities:

Entity 1, Nb23 129 residues - Formula weight is not available

1

GLN

VAL

GLN

LEU

GLN

GLU

SER

GLY

2

LEU

VAL

GLN

ALA

GLY

SER

LEU

ARG

LEU

3

SER

CYS

ALA

SER

GLY

ARG

THR

PHE

SER

4

SER

TYR

ALA

MET

ALA

TRP

PHE

ARG

GLN

ALA

5

PRO

GLY

LYS

GLU

ARG

GLU

PHE

VAL

ALA

ARG

6

ILE

SER

GLY

VAL

GLY

THR

ASN

THR

TYR

7

THR

ASP

SER

VAL

LYS

GLY

ARG

VAL

THR

ILE

8

SER

ARG

ASP

ASN

ALA

LYS

ASN

THR

VAL

TYR

9

LEU

GLN

MET

ASN

SER

LEU

LYS

PRO

GLU

ASP

10

THR

ALA

VAL

TYR

CYS

ALA

SER

ILE

11

TYR

GLY

TYR

SER

ASP

THR

SER

TYR

12

THR

ARG

LEU

ASN

TYR

LEU

TYR

TRP

GLY

13

GLN

GLY

THR

GLN

VAL

THR

VAL

SER

Samples:

sample_1: Nb23 monomer, [U-100% 13C; U-100% 15N], 250 uM; sodium phosphate 10 mM; D2O 5%; TRIS 19.5 mM; sodium chloride 21 mM

sample_2: Nb23 monomer, [U-100% 13C; U-100% 15N], 290 uM; sodium phosphate 10 mM; D2O 5%

sample_3: Nb23 monomer 190 uM; sodium phosphate 10 mM; D2O 5%; sodium chloride 6.3 mM

sample_4: Nb23 monomer 100 uM; sodium phosphate 10 mM; D2O 100%; sodium chloride 20 mM

sample_5: Nb23 monomer, [U-100% 13C; U-100% 15N], 175 uM; sodium phosphate 10 mM; D2O 100%

sample_conditions_1: pH: 6.95; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_2	isotropic	sample_conditions_1
3D CBCANH	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_2	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_3	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_3	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
2D HBCBCGCDHD	sample_5	isotropic	sample_conditions_1
2D HBCBCGCDCEHE	sample_5	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_4	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_5	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_5	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_5	isotropic	sample_conditions_1

Software:

NMRFAM-SPARKY - chemical shift assignment, chemical shift calculation, data analysis, peak picking

CS-Rosetta - structure solution

MolProbity - data analysis, geometry optimization

PONDEROSA - data analysis, geometry optimization, refinement, structure solution

ProcheckNMR - data analysis, geometry optimization

PyMOL - data analysis, geometry optimization, structure solution

TALOS-N - geometry optimization, structure solution

TOPSPIN - collection, data analysis, processing

NMR spectrometers:

Bruker AVANCE III 600 MHz

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