BMRB Entry 31020

Name: GFP Nanobody NMR Structure
Published: 2022-06-03

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PDB ID: 7v0v
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31020
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:

GFP Nanobody NMR Structure

Deposition date:

2022-05-11

Original release date:

2022-06-03

Authors:

Mueller, G.

Citation:

Citation: Fernandez-Quintero, M.; DeRose, E.; Gabel, S.; Mueller, G.; Liedl, K.. "Nanobody Paratope Ensembles in Solution Characterized by MD Simulations and NMR." Int. J. Mol. Sci. 23, 5419-5419 (2022).
PubMed: 35628231

Assembly members:

Assembly members:
entity_1, polymer, 123 residues, 13759.219 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 32630 Superkingdom: not available Kingdom: not available Genus/species: synthetic construct

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MAQVQLVESGGALVQPGGSL RLSCAASGFPVNRYSMRWYR QAPGKEREWVAGMSSAGDRS SYEDSVKGRFTISRDDARNT VYLQMNSLKPEDTAVYYCNV NVGFEYWGQGTQVTVSSHHH HHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	324
15N chemical shifts	110
1H chemical shifts	605

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_1 123 residues - 13759.219 Da.

1

MET

ALA

GLN

VAL

GLN

LEU

VAL

GLU

SER

GLY

2

GLY

ALA

LEU

VAL

GLN

PRO

GLY

SER

LEU

3

ARG

LEU

SER

CYS

ALA

SER

GLY

PHE

PRO

4

VAL

ASN

ARG

TYR

SER

MET

ARG

TRP

TYR

ARG

5

GLN

ALA

PRO

GLY

LYS

GLU

ARG

GLU

TRP

VAL

6

ALA

GLY

MET

SER

ALA

GLY

ASP

ARG

SER

7

SER

TYR

GLU

ASP

SER

VAL

LYS

GLY

ARG

PHE

8

THR

ILE

SER

ARG

ASP

ALA

ARG

ASN

THR

9

VAL

TYR

LEU

GLN

MET

ASN

SER

LEU

LYS

PRO

10

GLU

ASP

THR

ALA

VAL

TYR

CYS

ASN

VAL

11

ASN

VAL

GLY

PHE

GLU

TYR

TRP

GLY

GLN

GLY

12

THR

GLN

VAL

THR

VAL

SER

HIS

13

HIS

Samples:

sample_1: Anti-GFP Nanobody, [U-13C; U-15N], 1 mM

sample_conditions_1: ionic strength: 167.2 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HCCONH-TOCSY	sample_1	isotropic	sample_conditions_1
3D-CCONH-TOCSY	sample_1	isotropic	sample_conditions_1
3D CCH-TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D HBCBCGCDCDHE	sample_1	isotropic	sample_conditions_1
2D HBCBCGCDCDHE	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1

Software:

NMRView, Johnson, One Moon Scientific - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

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

NMR spectrometers:

Agilent DD2 800 MHz
Agilent DD2 600 MHz

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