BMRB Entry 30284

Name: Backbone structure of the Yersinia pestis outer membrane protein Ail in phospholipid bilayer nanodisc
Published: 2017-05-15

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PDB ID: 5vj8
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30284
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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:

Backbone structure of the Yersinia pestis outer membrane protein Ail in phospholipid bilayer nanodisc

Deposition date:

2017-04-19

Original release date:

2017-05-15

Authors:

Dutta, S.; Yong, Y.; Marassi, F.

Citation:

Citation: Dutta, S.; Yong, Y.; Marassi, F.. "Structural Insights into the Yersinia pestis Outer Membrane Protein Ail in Lipid Bilayers" J. Phys. Chem. B 121, 7561-7570 (2017).
PubMed: 28726410

Assembly members:

Assembly members:
entity_1, polymer, 156 residues, 17492.400 Da.

Natural source:

Natural source: Common Name: Yersinia pestis Taxonomy ID: 632 Superkingdom: Bacteria Kingdom: not available Genus/species: Yersinia pestis

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: EGESSISIGYAQSRVKEDGY KLDKNPRGFNLKYRYEFNND WGVIGSFAQTRRGFEESVDG FKLIDGDFKYYSVTAGPVFR INEYVSLYGLLGAGHGKAKF SSIFGQSESRSKTSLAYGAG LQFNPHPNFVIDASYEYSKL DDVKVGTWMLGAGYRF

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	94
15N chemical shifts	91
1H chemical shifts	91

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_1 156 residues - 17492.400 Da.

1

GLU

GLY

GLU

SER

ILE

SER

ILE

GLY

TYR

2

ALA

GLN

SER

ARG

VAL

LYS

GLU

ASP

GLY

TYR

3

LYS

LEU

ASP

LYS

ASN

PRO

ARG

GLY

PHE

ASN

4

LEU

LYS

TYR

ARG

TYR

GLU

PHE

ASN

ASP

5

TRP

GLY

VAL

ILE

GLY

SER

PHE

ALA

GLN

THR

6

ARG

GLY

PHE

GLU

SER

VAL

ASP

GLY

7

PHE

LYS

LEU

ILE

ASP

GLY

ASP

PHE

LYS

TYR

8

TYR

SER

VAL

THR

ALA

GLY

PRO

VAL

PHE

ARG

9

ILE

ASN

GLU

TYR

VAL

SER

LEU

TYR

GLY

LEU

10

LEU

GLY

ALA

GLY

HIS

GLY

LYS

ALA

LYS

PHE

11

SER

ILE

PHE

GLY

GLN

SER

GLU

SER

ARG

12

SER

LYS

THR

SER

LEU

ALA

TYR

GLY

ALA

GLY

13

LEU

GLN

PHE

ASN

PRO

HIS

PRO

ASN

PHE

VAL

14

ILE

ASP

ALA

SER

TYR

GLU

TYR

SER

LYS

LEU

15

ASP

VAL

LYS

VAL

GLY

THR

TRP

MET

LEU

16

GLY

ALA

GLY

TYR

ARG

PHE

Samples:

sample_1: Ail, [U-13C; U-15N; U-2H], 0.66 mM; DMPC 49.5 mM; DMPG 16.5 mM; sodium chloride 5 mM; sodium phosphate 25 mM

sample_conditions_1: ionic strength: 10 mM; pH: 6.5; pressure: 1 atm; temperature: 313 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N TROSY	sample_1	isotropic	sample_conditions_1
3D TROSY-HNCA	sample_1	isotropic	sample_conditions_1
3D 15N-NOESY	sample_1	isotropic	sample_conditions_1

Software:

CARA, Keller and Wuthrich - chemical shift assignment

TOPSPIN, Bruker Biospin - processing

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

NMR spectrometers:

Bruker AvanceIII 800 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