BMRB Entry 34424

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR34424
MolProbity Validation Chart

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Title:
Precursor structure of the self-processing module of iron-regulated FrpC of N. Meningitidis with calcium ions
Deposition date:
2019-08-14
Original release date:
2020-02-20
Authors:
Kuban, V.; Macek, P.; Hritz, J.; Nechvatalova, K.; Nedbalcova, K.; Faldyna, M.; Zidek, L.; Bumba, L.
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:
entity_1, polymer, 182 residues, 19246.879 Da.
entity_CA, non-polymer, 40.078 Da.

Natural source:

Natural source:   Common Name: Neisseria meningitidis   Taxonomy ID: 135720   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Neisseria meningitidis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli K-12

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSDALALDLDGDGIETVATK GFSGSLFDHNRDGIRTATGW VSADDGLLVRDLNGNGIIDN GAELFGDNTKLADGSFAKHG YAALAELDSNGDNIINAADA AFQSLRVWQDLNQDGISQAN ELRTLEELGIQSLDLAYKDV NKNLGNGNTLAQQGSYTKTN GTTAKMGDLLLAADNLHSRF LE

Data typeCount
13C chemical shifts576
15N chemical shifts156
1H chemical shifts933

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_2, 12
3entity_2, 22
4entity_2, 32
5entity_2, 42
6entity_2, 52

Entities:

Entity 1, entity_1 182 residues - 19246.879 Da.

1   GLYSERASPALALEUALALEUASPLEUASP
2   GLYASPGLYILEGLUTHRVALALATHRLYS
3   GLYPHESERGLYSERLEUPHEASPHISASN
4   ARGASPGLYILEARGTHRALATHRGLYTRP
5   VALSERALAASPASPGLYLEULEUVALARG
6   ASPLEUASNGLYASNGLYILEILEASPASN
7   GLYALAGLULEUPHEGLYASPASNTHRLYS
8   LEUALAASPGLYSERPHEALALYSHISGLY
9   TYRALAALALEUALAGLULEUASPSERASN
10   GLYASPASNILEILEASNALAALAASPALA
11   ALAPHEGLNSERLEUARGVALTRPGLNASP
12   LEUASNGLNASPGLYILESERGLNALAASN
13   GLULEUARGTHRLEUGLUGLULEUGLYILE
14   GLNSERLEUASPLEUALATYRLYSASPVAL
15   ASNLYSASNLEUGLYASNGLYASNTHRLEU
16   ALAGLNGLNGLYSERTYRTHRLYSTHRASN
17   GLYTHRTHRALALYSMETGLYASPLEULEU
18   LEUALAALAASPASNLEUHISSERARGPHE
19   LEUGLU

Entity 2, entity_2, 1 - Ca - 40.078 Da.

1   CA

Samples:

sample_1: TRIS 5 mM; sodium chloride 50 mM; sodium azide 0.1%; Calcium chloride 10 mM; P415A mutant of Self-processing module of FrpC, [U-99% 13C; U-99% 15N], 0.35 ± 0.05 mM

sample_2: TRIS 50 mM; sodium chloride 50 mM; sodium azide 0.1%; P415A mutant of Self-processing module of FrpC 0.707 ± 0.005 mM

sample_conditions_1: ionic strength: 65 mM; pH: 7.4; pressure: 1 atm; temperature: 303.2 K

sample_conditions_2: ionic strength: 100 mM; pH: 7.4; pressure: 1 atm; temperature: 303.2 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
1D WATERGATE W5sample_2isotropicsample_conditions_2

Software:

Sparky v3.115, Goddard - chemical shift assignment, data analysis, peak picking

TopSpin v3.2, Bruker Biospin - collection, processing

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

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

GROMACS v5.1.1, Erik Lindahl, David van der Spoel, Berk Hess, Mark Abraham - refinement

NMR spectrometers:

  • Bruker AVANCE III 600.05 MHz
  • Bruker AVANCE III 950.33 MHz
  • Bruker AVANCE III 850.28 MHz

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