BMRB Entry 19085

Name: Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.
Published: 2014-03-10

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PDB ID: 2m5x
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, SPARTA
BMRB Entry DOI: doi:10.13018/BMR19085
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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:

Novel method of protein purification for structural research. Example of ultra high resolution structure of SPI-2 inhibitor by X-ray and NMR spectroscopy.

Deposition date:

2013-03-12

Original release date:

2014-03-10

Authors:

Lenarcic Zivkovic, Martina; Dvornyk, Angela; Kludkiewicz, Barbara; Kopera, Edyta; Zagorski-Ostoja, Wlodzimierz; Grzelak, Krystyna; Zhukov, Igor; Bal, Wojciech

Citation:

Citation: Kopera, Edyta; Krzywda, Szymon; Lenarcic Zivkovic, Martina; Dvornyk, Angela; Kludkiewicz, Barbara; Grzelak, Krystyna; Zhukov, Igor; Zagorski-Ostoja, Wlodzimierz; Jaskolski, Mariusz; Bal, Wojciech. "Ultrahigh resolution protein structure enabled by a non-enzymatic tag removal method. X-ray and NMR study of SPI-2 inhibitor" .

Assembly members:

Assembly members:
GmSPI_2, polymer, 40 residues, 4317.768 Da.

Natural source:

Natural source: Common Name: Greater wax moth Taxonomy ID: 7137 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Galleria mellonella

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Pichia pastoris Vector: pPICZalfaB

Entity Sequences (FASTA):

Entity Sequences (FASTA):
GmSPI_2: EAAVCTTEWDPVCGKDGKTY SNLCWLNEAGVGLDHEGECL

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	96
15N chemical shifts	42
1H chemical shifts	241

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SPI-2 inhibitor	1

Entities:

Entity 1, SPI-2 inhibitor 40 residues - 4317.768 Da.

Non-native residues 1-3 and 40 originated from cloning procedures and protein processing in Pichia pastoris.

1	GLU	ALA	ALA	VAL	CYS	THR	THR	GLU	TRP	ASP
2	PRO	VAL	CYS	GLY	LYS	ASP	GLY	LYS	THR	TYR
3	SER	ASN	LEU	CYS	TRP	LEU	ASN	GLU	ALA	GLY
4	VAL	GLY	LEU	ASP	HIS	GLU	GLY	GLU	CYS	LEU

Samples:

sample_1: GmSPI 2 0.5 mM

sample_conditions_1: ionic strength: 50 mM; pH: 4.5; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-1H TOCSY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	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

Software:

No software information available

NMR spectrometers:

Varian Uniform NMR System 800 MHz

UNP	Q968S7
BMRB	16703 16704 16705
PDB	2M5X 4HGU
GB	AAK48526
AlphaFold	Q968S7

1	GLU	ALA	ALA	VAL	CYS	THR	THR	GLU	TRP	ASP
2	PRO	VAL	CYS	GLY	LYS	ASP	GLY	LYS	THR	TYR
3	SER	ASN	LEU	CYS	TRP	LEU	ASN	GLU	ALA	GLY
4	VAL	GLY	LEU	ASP	HIS	GLU	GLY	GLU	CYS	LEU

1	GLU	ALA	ALA	VAL	CYS	THR	THR	GLU	TRP	ASP
2	PRO	VAL	CYS	GLY	LYS	ASP	GLY	LYS	THR	TYR
3	SER	ASN	LEU	CYS	TRP	LEU	ASN	GLU	ALA	GLY
4	VAL	GLY	LEU	ASP	HIS	GLU	GLY	GLU	CYS	LEU