BMRB Entry 17768

Name: Structure of bacteriophage SPP1 gp17 protein
Published: 2012-05-09

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PDB ID: 2lfp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR17768
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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:

Structure of bacteriophage SPP1 gp17 protein

Deposition date:

2011-07-07

Original release date:

2012-05-09

Authors:

Chagot, Benjamin; Auzat, Isabelle; Gallopin, Matthieu; Petitpas, Isabelle; Gilquin, Bernard; Tavares, Paulo; Zinn-Justin, Sophie

Citation:

Citation: Chagot, Benjamin; Auzat, Isabelle; Gallopin, Matthieu; Petitpas, Isabelle; Gilquin, Bernard; Tavares, Paulo; Zinn-Justin, Sophie. "Solution structure of gp17 from the Siphoviridae bacteriophage SPP1: insights into its role in virion assembly." Proteins 80, 319-326 (2012).
PubMed: 22072538

Assembly members:

Assembly members:
gp17, polymer, 139 residues, 15478.582 Da.

Natural source:

Natural source: Common Name: Bacteriophage SPP1 Taxonomy ID: 10724 Superkingdom: Viruses Kingdom: not available Genus/species: Lambda-like viruses Bacteriophage SPP1

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: N/A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
gp17: QGLQTWKLASRALQKATVEN LESYQPLMEMVNQVTESPGK DDPYPYVVIGDQSSTPFETK SSFGENITMDFHVWGGTTRA EAQDISSRVLEALTYKPLMF EGFTFVAKKLVLAQVITDTD GVTKHGIIKVRFTINNNTG

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	282
15N chemical shifts	102
1H chemical shifts	708

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	gp17	1

Entities:

Entity 1, gp17 139 residues - 15478.582 Da.

First four residues (QGLQ) and the two last (TG) are cloning artefacts

1

GLN

GLY

LEU

GLN

THR

TRP

LYS

LEU

ALA

SER

2

ARG

ALA

LEU

GLN

LYS

ALA

THR

VAL

GLU

ASN

3

LEU

GLU

SER

TYR

GLN

PRO

LEU

MET

GLU

MET

4

VAL

ASN

GLN

VAL

THR

GLU

SER

PRO

GLY

LYS

5

ASP

PRO

TYR

PRO

TYR

VAL

ILE

GLY

6

ASP

GLN

SER

THR

PRO

PHE

GLU

THR

LYS

7

SER

PHE

GLY

GLU

ASN

ILE

THR

MET

ASP

8

PHE

HIS

VAL

TRP

GLY

THR

ARG

ALA

9

GLU

ALA

GLN

ASP

ILE

SER

ARG

VAL

LEU

10

GLU

ALA

LEU

THR

TYR

LYS

PRO

LEU

MET

PHE

11

GLU

GLY

PHE

THR

PHE

VAL

ALA

LYS

LEU

12

VAL

LEU

ALA

GLN

VAL

ILE

THR

ASP

THR

ASP

13

GLY

VAL

THR

LYS

HIS

GLY

ILE

LYS

VAL

14

ARG

PHE

THR

ILE

ASN

THR

GLY

Samples:

sample_1: gp17, [U-100% 13C; U-100% 15N], 0.3 mM; H2O 90%; D2O 10%; TRIS 50 mM; sodium chloride 50 mM

sample_2: gp17 0.3 mM; H2O 90%; D2O 10%; MES 50 mM; sodium chloride 500 mM

sample_3: gp17, [U-100% 13C; U-100% 15N], 0.6 mM; H2O 90%; D2O 10%; MES 50 mM; sodium chloride 500 mM

sample_conditions_1: ionic strength: 0.05 M; pH: 7.5; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 0.5 M; pH: 6.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1
3D HN(CA)CO	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H COSY	sample_2	isotropic	sample_conditions_2
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_2
T1 relaxation	sample_3	isotropic	sample_conditions_2
T2 relaxation	sample_3	isotropic	sample_conditions_2
heteronuclear NOE	sample_3	isotropic	sample_conditions_2

Software:

TOPSPIN v1.3, Bruker Biospin - collection, processing

SPARKY v1.3, Goddard - chemical shift assignment

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

NMR spectrometers:

Bruker AMX 700 MHz
Bruker AMX 600 MHz

PDB	2LFP 5A20 5A21
EMBL	CAA66549
REF	NP_690679