BMRB Entry 30679

Name: Gypsy Moth Pheromone-binding protein 1 (LdisPBP1) NMR Structure at pH 4.5
Published: 2020-09-18

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PDB ID: 6um9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30679
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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:

Gypsy Moth Pheromone-binding protein 1 (LdisPBP1) NMR Structure at pH 4.5

Deposition date:

2019-10-09

Original release date:

2020-09-18

Authors:

Terrado, M.; Plettner, E.

Citation:

Citation: Terrado, Mailyn; Okon, Mark; McIntosh, Lawrence; Plettner, Erika. "Ligand- and pH-Induced Structural Transition of Gypsy Moth Lymantria dispar Pheromone-Binding Protein 1 (LdisPBP1)" Biochemistry 57, 3411-3426 (2020).
PubMed: 32877603

Assembly members:

Assembly members:
entity_1, polymer, 143 residues, 16165.910 Da.

Natural source:

Natural source: Common Name: Gypsy moth Taxonomy ID: 13123 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Lymantria dispar

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET 30 Xa/LIC

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SKEVMKQMTINFAKPMEACK QELNVPDAVMQDFFNFWKEG YQITNREAGCVILCLAKKLE LLDQDMNLHHGKAMEFAMKH GADEAMAKQLLDIKHSCEKV ITIVADDPCQTMLNLAMCFK AEIHKLDWAPTLDVAVGELL ADT

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	610
15N chemical shifts	156
1H chemical shifts	980

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 143 residues - 16165.910 Da.

1

SER

LYS

GLU

VAL

MET

LYS

GLN

MET

THR

ILE

2

ASN

PHE

ALA

LYS

PRO

MET

GLU

ALA

CYS

LYS

3

GLN

GLU

LEU

ASN

VAL

PRO

ASP

ALA

VAL

MET

4

GLN

ASP

PHE

ASN

PHE

TRP

LYS

GLU

GLY

5

TYR

GLN

ILE

THR

ASN

ARG

GLU

ALA

GLY

CYS

6

VAL

ILE

LEU

CYS

LEU

ALA

LYS

LEU

GLU

7

LEU

ASP

GLN

ASP

MET

ASN

LEU

HIS

8

GLY

LYS

ALA

MET

GLU

PHE

ALA

MET

LYS

HIS

9

GLY

ALA

ASP

GLU

ALA

MET

ALA

LYS

GLN

LEU

10

LEU

ASP

ILE

LYS

HIS

SER

CYS

GLU

LYS

VAL

11

ILE

THR

ILE

VAL

ALA

ASP

PRO

CYS

GLN

12

THR

MET

LEU

ASN

LEU

ALA

MET

CYS

PHE

LYS

13

ALA

GLU

ILE

HIS

LYS

LEU

ASP

TRP

ALA

PRO

14

THR

LEU

ASP

VAL

ALA

VAL

GLY

GLU

LEU

15

ALA

ASP

THR

Samples:

sample_1: LdisPBP1, [U-99% 13C; U-99% 15N], 1.2 M; sodium acetate 50 mM; EDTA 1 mM; sodium azide 0.05 % w/v

sample_conditions_1: pH: 4.5; pressure: 1 atm; temperature: 308 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	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:

NMRe, Ryu H, Lim GT, Sung BH, Lee J - refinement

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Sparky, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 850 MHz

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