BMRB Entry 30246

Name: Red abalone lysin F104A
Published: 2018-01-25

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PDB ID: 5utg
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30246
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:

Red abalone lysin F104A

Deposition date:

2017-02-14

Original release date:

2018-01-25

Authors:

Wilburn, D.; Tuttle, L.

Citation:

Citation: Wilburn, D.; Tuttle, L.; Klevit, R.; Swanson, W.. "Solution structure of sperm lysin yields novel insights into molecular dynamics of rapid protein evolution" Proc. Natl. Acad. Sci. U. S. A. 115, 1310-1315 (2018).
PubMed: 29348201

Assembly members:

Assembly members:
entity_1, polymer, 135 residues, 16089.939 Da.

Natural source:

Natural source: Common Name: California red abalone Taxonomy ID: 6454 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Haliotis rufescens

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli K-12 Vector: pET11d

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GRSWHYVEPKFLNKAFEVAL KVQIIAGFDRGLVKWLRVHG RTLSTVQKKALYFVNRRYMQ THWANYMLWINKKIDALGRT PVVGDYTRLGAEIGRRIDMA YFYDALKDKNMIPKYLPYME EINRMRPADVPVKYM

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	454
15N chemical shifts	119
1H chemical shifts	662

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_1 135 residues - 16089.939 Da.

1

GLY

ARG

SER

TRP

HIS

TYR

VAL

GLU

PRO

LYS

2

PHE

LEU

ASN

LYS

ALA

PHE

GLU

VAL

ALA

LEU

3

LYS

VAL

GLN

ILE

ALA

GLY

PHE

ASP

ARG

4

GLY

LEU

VAL

LYS

TRP

LEU

ARG

VAL

HIS

GLY

5

ARG

THR

LEU

SER

THR

VAL

GLN

LYS

ALA

6

LEU

TYR

PHE

VAL

ASN

ARG

TYR

MET

GLN

7

THR

HIS

TRP

ALA

ASN

TYR

MET

LEU

TRP

ILE

8

ASN

LYS

ILE

ASP

ALA

LEU

GLY

ARG

THR

9

PRO

VAL

GLY

ASP

TYR

THR

ARG

LEU

GLY

10

ALA

GLU

ILE

GLY

ARG

ILE

ASP

MET

ALA

11

TYR

PHE

TYR

ASP

ALA

LEU

LYS

ASP

LYS

ASN

12

MET

ILE

PRO

LYS

TYR

LEU

PRO

TYR

MET

GLU

13

GLU

ILE

ASN

ARG

MET

ARG

PRO

ALA

ASP

VAL

14

PRO

VAL

LYS

TYR

MET

Samples:

sample_1: lysin, [U-15N], 300 uM; sodium chloride, natural abundunce, 200 mM; sodium phosphate 10 mM

sample_2: lysin, [U-13C; U-15N], 300 uM; sodium chloride 200 mM; sodium phosphate 10 mM

sample_3: c12e6/hexanol 5 w/v; lysin, [U-15N], 300 uM; sodium chloride 200 mM; sodium phosphate 10 mM

sample_4: Tris 10 mM; lysin, [U-13C; U-15N], 200 uM; sodium chloride 200 mM

sample_conditions_1: ionic strength: 200 mM; pH: 7.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N hetNOE	sample_1	isotropic	sample_conditions_1
2D 1H-15N T1	sample_1	isotropic	sample_conditions_1
2D 1H-15N T2	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_2	isotropic	sample_conditions_1
3D HNCA	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC-IPAP	sample_3	anisotropic	sample_conditions_1
3D HNCO	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D HN(CO)CACB	sample_2	isotropic	sample_conditions_1
3D HNCACB	sample_2	isotropic	sample_conditions_1
3D HN(CO)CA	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_2	isotropic	sample_conditions_1

Software:

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

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

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN, Bruker Biospin - collection

X-PLOR NIH v2.43, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE 500 MHz
Bruker AVANCE 600 MHz

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