BMRB Entry 34139

Name: LysF1 sh3b domain structure
Published: 2017-09-15

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PDB ID: 5o1q
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34139
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Nicholas Rego and David Koes
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Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: LysF1 sh3b domain structure PubMed: 28852930

Deposition date: 2017-05-19 Original release date: 2017-09-15

Authors: Benesik, M.; Novacek, J.; Janda, L.; Dopitova, R.; Pernisova, M.; Melkova, K.; Tisakova, L.; Doskar, J.; Zidek, L.; Hejatko, J.; Pantucek, R.

Citation: Benesik, M.; Novacek, J.; Janda, L.; Dopitova, R.; Pernisova, M.; Melkova, K.; Tisakova, L.; Doskar, J.; Zidek, L.; Hejatko, J.; Pantucek, R.. "Role of SH3b binding domain in a natural deletion mutant of Kayvirus endolysin LysF1 with a broad range of lytic activity." Virus Genes 54, 130-139 (2018).

Assembly members:
entity_1, polymer, 106 residues, 11530.995 Da.

Natural source: Common Name: Kayvirus Taxonomy ID: 1857843 Superkingdom: Viruses Kingdom: not available Genus/species: Kayvirus not available

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

Entity Sequences (FASTA):
entity_1: ETPATRPVTGSWKKNQYGTW YKPENATFVNGNQPIVTRIG SPFLNAPVGGNLPAGATIVY DEVCIQAGHIWIGYNAYNGN RVYCPVRTCQGVPPNQIPGV AWGVFK

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	439
15N chemical shifts	111
1H chemical shifts	695

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_1 106 residues - 11530.995 Da.

1

GLU

THR

PRO

ALA

THR

ARG

PRO

VAL

THR

GLY

2

SER

TRP

LYS

ASN

GLN

TYR

GLY

THR

TRP

3

TYR

LYS

PRO

GLU

ASN

ALA

THR

PHE

VAL

ASN

4

GLY

ASN

GLN

PRO

ILE

VAL

THR

ARG

ILE

GLY

5

SER

PRO

PHE

LEU

ASN

ALA

PRO

VAL

GLY

6

ASN

LEU

PRO

ALA

GLY

ALA

THR

ILE

VAL

TYR

7

ASP

GLU

VAL

CYS

ILE

GLN

ALA

GLY

HIS

ILE

8

TRP

ILE

GLY

TYR

ASN

ALA

TYR

ASN

GLY

ASN

9

ARG

VAL

TYR

CYS

PRO

VAL

ARG

THR

CYS

GLN

10

GLY

VAL

PRO

ASN

GLN

ILE

PRO

GLY

VAL

11

ALA

TRP

GLY

VAL

PHE

LYS

Samples:

sample_1: Na-phosphate 20 mM; sh3b domain, [U-99% 13C; U-99% 15N], 0.25 mM

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	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 HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNH NOESY	sample_1	isotropic	sample_conditions_1
3D HCH NOESY	sample_1	isotropic	sample_conditions_1
3D HCH NOESY	sample_1	isotropic	sample_conditions_1
1D H	sample_1	isotropic	sample_conditions_1

Software:

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

SPARKY, Goddard - chemical shift assignment

TOPSPIN, Bruker Biospin - collection

ARIA, Linge, O'Donoghue and Nilges - structure calculation

NMR spectrometers:

Bruker AvanceII 600 MHz
Bruker AvanceII 950 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts