BMRB Entry 28058

Name: NMR assignment of self-processing module of FrpC protein of Neisseria meningitidis loaded with calcium ions
Published: 2020-02-20

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PDB ID: 6sjw
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR28058
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:

NMR assignment of self-processing module of FrpC protein of Neisseria meningitidis loaded with calcium ions

Deposition date:

2020-01-02

Original release date:

2020-02-20

Authors:

Kuban, Vojtech; Zidek, Lukas; Macek, Pavel; Hritz, Jozef; Bumba, Ladislav; M., Faldyna; K., Nedbalcova; K., Nechvatalova

Citation:

Citation: Kuban, V.; Macek, P.; Hritz, J.; Nechvatalova, K.; Nedbalcova, K.; Faldyna, M.; Zidek, L.; Bumba, L.. "Structural basis of Ca 2+ -dependent self-processing activity of repeat-in-toxin proteins" mBio 11, e00226-20-e00226-20 (2020).
PubMed: 32184239

Assembly members:

Assembly members:
SPM, polymer, 179 residues, Formula weight is not available
entity_CA, non-polymer, 40.078 Da.

Natural source:

Natural source: Common Name: Neisseria meningitidis Taxonomy ID: 487 Superkingdom: Bacteria Kingdom: not available Genus/species: Neisseria meningitidis

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pSPM-His

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SPM: PLALDLDGDGIETVATKGFS GSLFDHNRDGIRTATGWVSA DDGLLVRDLNGNGIIDNGAE LFGDNTKLADGSFAKHGYAA LAELDSNGDNIINAADAAFQ SLRVWQDLNQDGISQANELR TLEELGIQSLDLAYKDVNKN LGNGNTLAQQGSYTKTNGTT AKMGDLLLAADNLHSRFLE

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1
spectral_peak_list

Data type	Count
13C chemical shifts	608
15N chemical shifts	162
1H chemical shifts	974
T1 relaxation values	124
T2 relaxation values	124
heteronuclear NOE values	124

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SPM	1
2	CA	2

Entities:

Entity 1, SPM 179 residues - Formula weight is not available

1

PRO

LEU

ALA

LEU

ASP

LEU

ASP

GLY

ASP

GLY

2

ILE

GLU

THR

VAL

ALA

THR

LYS

GLY

PHE

SER

3

GLY

SER

LEU

PHE

ASP

HIS

ASN

ARG

ASP

GLY

4

ILE

ARG

THR

ALA

THR

GLY

TRP

VAL

SER

ALA

5

ASP

GLY

LEU

VAL

ARG

ASP

LEU

ASN

6

GLY

ASN

GLY

ILE

ASP

ASN

GLY

ALA

GLU

7

LEU

PHE

GLY

ASP

ASN

THR

LYS

LEU

ALA

ASP

8

GLY

SER

PHE

ALA

LYS

HIS

GLY

TYR

ALA

9

LEU

ALA

GLU

LEU

ASP

SER

ASN

GLY

ASP

ASN

10

ILE

ASN

ALA

ASP

ALA

PHE

GLN

11

SER

LEU

ARG

VAL

TRP

GLN

ASP

LEU

ASN

GLN

12

ASP

GLY

ILE

SER

GLN

ALA

ASN

GLU

LEU

ARG

13

THR

LEU

GLU

LEU

GLY

ILE

GLN

SER

LEU

14

ASP

LEU

ALA

TYR

LYS

ASP

VAL

ASN

LYS

ASN

15

LEU

GLY

ASN

GLY

ASN

THR

LEU

ALA

GLN

16

GLY

SER

TYR

THR

LYS

THR

ASN

GLY

THR

17

ALA

LYS

MET

GLY

ASP

LEU

ALA

18

ASP

ASN

LEU

HIS

SER

ARG

PHE

LEU

GLU

Entity 2, CA - Ca - 40.078 Da.

1

CA

Samples:

sample_1: SPM, [U-100% 13C; U-100% 15N], 0.4 mM; TRIS 5 mM; sodium chloride 50 mM; sodium azide 0.1%; Calcium chloride 10 mM

sample_conditions_1: ionic strength: 65 mM; pH: 7.4; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
2D R2 15N,1H correlation	sample_1	isotropic	sample_conditions_1
2D R1 15N,1H correlation	sample_1	isotropic	sample_conditions_1
2D NOE 15N,1H correlation	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3.115, Goddard - chemical shift assignment, peak picking

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

TOPSPIN v3.2, Bruker Biospin - collection

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 850 MHz
Bruker Avance 950 MHz

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