BMRB Entry 19553

Name: NMR solution structure of chitin-binding domain from dust mite group XII allergen Blo t 12.
Published: 2014-11-17

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PDB ID: 2mfk
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19553
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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:

NMR solution structure of chitin-binding domain from dust mite group XII allergen Blo t 12.

Deposition date:

2013-10-15

Original release date:

2014-11-17

Authors:

Naik, Mandar; Kung, Camy; Huang, Tai-huang

Citation:

Citation: Naik, Mandar; Kung, Camy; Huang, Tai-huang. "Solution structure of Blo 1 12 CBD domain." .

Assembly members:

Assembly members:
entity, polymer, 69 residues, 7528.702 Da.

Natural source:

Natural source: Common Name: Storage mite Taxonomy ID: 40697 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Blomia tropicalis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pGEX6P-3

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GPLGSDLIVHEGGKTYHVVC HEEGPIPHPGNVHKYIICSK SGSLWYITVMPCSIGTKFDP ISRNCVLDN

Data sets:

assigned_chemical_shifts
- CBD

Data type	Count
13C chemical shifts	292
15N chemical shifts	66
1H chemical shifts	468

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	Blo 1 12 CBD domain	1

Entities:

Entity 1, Blo 1 12 CBD domain 69 residues - 7528.702 Da.

Residue 75 to 79 are non-native leftover of purification tag.

1

GLY

PRO

LEU

GLY

SER

ASP

LEU

ILE

VAL

HIS

2

GLU

GLY

LYS

THR

TYR

HIS

VAL

CYS

3

HIS

GLU

GLY

PRO

ILE

PRO

HIS

PRO

GLY

4

ASN

VAL

HIS

LYS

TYR

ILE

CYS

SER

LYS

5

SER

GLY

SER

LEU

TRP

TYR

ILE

THR

VAL

MET

6

PRO

CYS

SER

ILE

GLY

THR

LYS

PHE

ASP

PRO

7

ILE

SER

ARG

ASN

CYS

VAL

LEU

ASP

ASN

Samples:

CN: Blo t 12 CBD, [U-100% 13C; U-100% 15N], 1 ± 0.05 mM; potassium phosphate 50 ± 1 mM; sodium chloride 100 ± 1 mM; H2O 90 ± 1 %; D2O 10 ± 1 %

N: Blo t 12 CBD, [U-100% 15N], 1 ± 0.05 mM; potassium phosphate 50 ± 1 mM; sodium chloride 100 ± 1 mM; H2O 90 ± 1 %; D2O 10 ± 1 %

Phage: Blo t 12 CBD, [U-100% 15N], 1 ± 0.05 mM; potassium phosphate 50 ± 1 mM; sodium chloride 100 ± 1 mM; Pf1 phage 11 ± 0.1 mg/ml; H2O 90 ± 0.1 %; D2O 10 ± 0.1 %

Default: pH: 6.0; pressure: 1 atm; temperature: 295 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	N	isotropic	Default
2D 1H-13C HSQC	CN	isotropic	Default
3D HNCO	CN	isotropic	Default
3D HNCA	CN	isotropic	Default
3D HNCACB	CN	isotropic	Default
3D CBCA(CO)NH	CN	isotropic	Default
3D HccoNH	CN	isotropic	Default
3D CCcoNH	CN	isotropic	Default
3D HCCH-COSY	CN	isotropic	Default
3D HBHAcoNH	CN	isotropic	Default
2D-hbCBcgcdHD	CN	isotropic	Default
3D 1H-13C NOESYHSQC	CN	isotropic	Default
3D 1H-15N NOESYHSQC	CN	isotropic	Default
2D 1H-15N IPAP HSQC	Phage	anisotropic	Default

Software:

TOPSPIN v3.0, Bruker Biospin - collection, processing

SPARKY, Goddard - chemical shift assignment, peak picking

CYANA v3.9, Guntert, Mumenthaler and Wuthrich - geometry optimization, structure solution

PSVS v1.5, Bhattacharya and Montelione - validation

X-PLOR NIH v2.34, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker Avance 500 MHz
Bruker Avance 600 MHz

PDB	2MFK
GB	AAQ55550