BMRB Entry 31164

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31164

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Title:
Solution structure of the hemoglobin receptor HbpA from Corynebacterium diphtheriae
Deposition date:
2024-04-09
Original release date:
2025-01-28
Authors:
Mahoney, B.; Clubb, R.
Citation:

Citation: Mahoney, B.; Lyman, L.; Ford, J.; Soule, J.; Goring, A.; Collazo, M.; Cascio, D.; Ton-That, H.; Schmitt, M.; Clubb, R.. "The Corynebacterium diphtheriae HbpA receptor binds hemoglobin using a novel structured domain"  .

Assembly members:

Assembly members:
entity_1, polymer, 198 residues, 21918.514 Da.

Natural source:

Natural source:   Common Name: Corynebacterium diphtheriae NCTC 13129   Taxonomy ID: 257309   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Corynebacterium diphtheriae

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)   Vector: pMAPLe4

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: SEEVKNADLYWGFSGSSHHK YDHNGPKFEKAGKGAELTNI DAASAYAETFKKGVFPNNKR EKSDILVFHNGEVKTETNHS SYQINWPGEVTMKLGYGDGL VIKDLNLMLKNGNMGELKAT VGENSNITLFDVQEYSVSDN TITVTPKIPPCTTGTWKPWH NDLTSKLGSLKSVFFESYTC NNDDIAKKPLPLTVVLNG

Data sets:
Data typeCount
13C chemical shifts795
15N chemical shifts176
1H chemical shifts1105

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11

Entities:

Entity 1, unit_1 198 residues - 21918.514 Da.

1   SERGLUGLUVALLYSASNALAASPLEUTYR
2   TRPGLYPHESERGLYSERSERHISHISLYS
3   TYRASPHISASNGLYPROLYSPHEGLULYS
4   ALAGLYLYSGLYALAGLULEUTHRASNILE
5   ASPALAALASERALATYRALAGLUTHRPHE
6   LYSLYSGLYVALPHEPROASNASNLYSARG
7   GLULYSSERASPILELEUVALPHEHISASN
8   GLYGLUVALLYSTHRGLUTHRASNHISSER
9   SERTYRGLNILEASNTRPPROGLYGLUVAL
10   THRMETLYSLEUGLYTYRGLYASPGLYLEU
11   VALILELYSASPLEUASNLEUMETLEULYS
12   ASNGLYASNMETGLYGLULEULYSALATHR
13   VALGLYGLUASNSERASNILETHRLEUPHE
14   ASPVALGLNGLUTYRSERVALSERASPASN
15   THRILETHRVALTHRPROLYSILEPROPRO
16   CYSTHRTHRGLYTHRTRPLYSPROTRPHIS
17   ASNASPLEUTHRSERLYSLEUGLYSERLEU
18   LYSSERVALPHEPHEGLUSERTYRTHRCYS
19   ASNASNASPASPILEALALYSLYSPROLEU
20   PROLEUTHRVALVALLEUASNGLY

Samples:

sample_1: Hemoglobin receptor HbpA, [U-100% 13C; U-100% 15N], 0.72 ± 0.02 mM; sodium phosphate 50 ± 1 mM; sodium chloride 100 ± 2 mM

sample_2: Hemoglobin receptor HbpA, [U-100% 13C; U-100% 15N], 0.72 ± 0.02 mM; sodium phosphate 50 ± 1 mM; sodium chloride 100 ± 2 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.2; pressure: 1 atm; temperature: 295 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_2isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_2isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1

Software:

CARA v1.9.1.7, Keller and Wuthrich - chemical shift assignment

X-PLOR NIH v3.6, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

Xipp v1.21.7, Dan Garrett - chemical shift assignment, peak picking

UNIO v10, Torsten Herrmann - structure calculation

TopSpin, Bruker Biospin - collection

NMRPipe v11.1, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRFAM-SPARKY, National Magnetic Resonance Facility at Madison (Wisconsin) - data analysis

TALOS-N, Cornilescu, Delaglio and Bax - geometry optimization

PROCHECK / PROCHECK-NMR, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - geometry optimization

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz
  • Bruker AVANCE NEO 800 MHz
  • Bruker AVANCE DRX 500 MHz

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