BMRB Entry 30094

Name: Solid-state MAS NMR structure of Acinetobacter phage 205 (AP205) coat protein in assembled capsid particles
Published: 2016-08-08

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PDB ID: 5jzr
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30094
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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:

Solid-state MAS NMR structure of Acinetobacter phage 205 (AP205) coat protein in assembled capsid particles

Deposition date:

2016-05-17

Original release date:

2016-08-08

Authors:

Jaudzems, K.; Andreas, L.; Stanek, J.; Lalli, D.; Bertarello, A.; Le Marchand, T.; Cala-De Paepe, D.; Kotelovica, S.; Akopjana, I.; Knott, B.; Wegner, S.; Engelke, F.; Lesage, A.; Emsley, L.; Tars, K.; Herrmann, T.; Pintacuda, G.

Citation:

Citation: Andreas, Loren; Jaudzems, Kristaps; Stanek, Jan; Lalli, Daniela; Bertarello, Andrea; Marchand, Tanguy; Paepe, Diane; Kotelovica, Svetlana; Akopjana, Inara; Knott, Benno; Wegner, Sebastian; Engelke, Frank; Lesage, Anne; Emsley, Lyndon; Tars, Kaspars; Herrmann, Torsten; Pintacuda, Guido. "Structure of fully protonated proteins by proton-detected magic-angle spinning NMR" Proc. Natl. Acad. Sci. U. S. A. 113, 9187-9192 (2016).
PubMed: 27489348

Assembly members:

Assembly members:
Coat protein, polymer, 131 residues, 14022.842 Da.

Natural source:

Natural source: Common Name: Acinetobacter phage AP205 Taxonomy ID: 154784 Superkingdom: Viruses Kingdom: Levivirus Genus/species: not available not available

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Coat protein: MANKPMQPITSTANKIVWSD PTRLSTTFSASLLRQRVKVG IAELNNVSGQYVSVYKRPAP KPEGCADACVIMPNENQSIR TVISGSAENLATLKAEWETH KRNVDTLFASGNAGLGFLDP TAAIVSSDTTA

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	377
15N chemical shifts	101
1H chemical shifts	539

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1, chain 1	1
2	entity_1, chain 2	1

Entities:

Entity 1, entity_1, chain 1 131 residues - 14022.842 Da.

1

MET

ALA

ASN

LYS

PRO

MET

GLN

PRO

ILE

THR

2

SER

THR

ALA

ASN

LYS

ILE

VAL

TRP

SER

ASP

3

PRO

THR

ARG

LEU

SER

THR

PHE

SER

ALA

4

SER

LEU

ARG

GLN

ARG

VAL

LYS

VAL

GLY

5

ILE

ALA

GLU

LEU

ASN

VAL

SER

GLY

GLN

6

TYR

VAL

SER

VAL

TYR

LYS

ARG

PRO

ALA

PRO

7

LYS

PRO

GLU

GLY

CYS

ALA

ASP

ALA

CYS

VAL

8

ILE

MET

PRO

ASN

GLU

ASN

GLN

SER

ILE

ARG

9

THR

VAL

ILE

SER

GLY

SER

ALA

GLU

ASN

LEU

10

ALA

THR

LEU

LYS

ALA

GLU

TRP

GLU

THR

HIS

11

LYS

ARG

ASN

VAL

ASP

THR

LEU

PHE

ALA

SER

12

GLY

ASN

ALA

GLY

LEU

GLY

PHE

LEU

ASP

PRO

13

THR

ALA

ILE

VAL

SER

ASP

THR

14

ALA

Samples:

sample_1: AP205 coat protein, [U-100% 13C; U-100% 15N], 500 ± 200 mg/mL; HEPES 5 ± 1 mM; PEG, [U-2H], 15 ± 5 %; sodium chloride 50 ± 5 mM

sample_conditions_1: ionic strength: 0.055 M; pH: 7.5; pressure: 1 atm; temperature: 283 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HhNH	sample_1	isotropic	sample_conditions_1
3D HhCH	sample_1	isotropic	sample_conditions_1
3D HcCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D hCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D hNCAH	sample_1	isotropic	sample_conditions_1
3D hNcoCAH	sample_1	isotropic	sample_conditions_1
3D hCOCAH	sample_1	isotropic	sample_conditions_1
3D hCANH	sample_1	isotropic	sample_conditions_1
3D hCOnCAH	sample_1	isotropic	sample_conditions_1
3D hcoCAcoNH	sample_1	isotropic	sample_conditions_1

Software:

CARA v1.9, Keller and Wuthrich - chemical shift assignment

CYANA v3.97, Guntert, Mumenthaler and Wuthrich - structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

TOPSPIN v3.5, Bruker Biospin - collection, processing

UNIO v2.6, Torsten Herrmann et al. - structure calculation

NMR spectrometers:

Bruker AvanceIII 1000 MHz

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