BMRB Entry 30040

Name: Cell surface anchoring domain
Published: 2017-06-22

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PDB ID: 5ix9
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30040
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:

Cell surface anchoring domain

Deposition date:

2016-03-23

Original release date:

2017-06-22

Authors:

Guo, S.; Langelaan, D.

Citation:

Citation: Guo, Shuaiqi; Stevens, Corey; Vance, Tyler; Olijve, Luuk; Graham, Laurie; Campbell, Robert; Yazdi, Saeed; Escobedo, Carlos; Bar-Dolev, Maya; Yashunsky, Victor; Braslavsky, Ido; Langelaan, David; Smith, Steven; Allingham, John; Voets, Ilja; Davies, Peter. "Structure of a 1.5-MDa adhesin that binds its Antarctic bacterium to diatoms and ice" Sci. Adv. 3, e1701440-e1701440 (2017).
PubMed: 28808685

Assembly members:

Assembly members:
Antifreeze protein, polymer, 76 residues, 7826.605 Da.

Natural source:

Natural source: Common Name: g-proteobacteria Taxonomy ID: 178399 Superkingdom: Bacteria Kingdom: not available Genus/species: Marinomonas primoryensis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Antifreeze protein: GNAIGFITKLDGSVTVQSIN GQERVLKLGDPIFFGETVLT GGSGSVTIAFVDGTDVVIGG DSIVEMTDEIYNTGDN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	317
15N chemical shifts	82
1H chemical shifts	490

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 76 residues - 7826.605 Da.

1

GLY

ASN

ALA

ILE

GLY

PHE

ILE

THR

LYS

LEU

2

ASP

GLY

SER

VAL

THR

VAL

GLN

SER

ILE

ASN

3

GLY

GLN

GLU

ARG

VAL

LEU

LYS

LEU

GLY

ASP

4

PRO

ILE

PHE

GLY

GLU

THR

VAL

LEU

THR

5

GLY

SER

GLY

SER

VAL

THR

ILE

ALA

PHE

6

VAL

ASP

GLY

THR

ASP

VAL

ILE

GLY

7

ASP

SER

ILE

VAL

GLU

MET

THR

ASP

GLU

ILE

8

TYR

ASN

THR

GLY

ASP

ASN

Samples:

sample_1: CaCl2 2 mM; MgCl2 2 mM; MpAFP_RINM, [U-13C], 3 mM; TRIS 20 mM; sodium chloride 50 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 50 mM; pH: 6.5; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1

Software:

ARIA, Linge, O'Donoghue and Nilges - refinement

Analysis, CCPN - chemical shift assignment

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

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

VNMR, Varian - collection

NMR spectrometers:

Varian INOVA 600 MHz

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