BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules 		Member of WWPDB

BMRB Entry 25113

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25113

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Title: Domain Orientation and Dynamics of the 38.8 kDa Staphylococcus aureus Hemoglobin Receptor, IsdH   PubMed: 25687963

Deposition date: 2014-07-29 Original release date: 2022-05-12

Authors: Sjodt, Megan; Macdonald, Ramsay; Spirig, Thomas; Clubb, Robert

Citation: Sjodt, Megan; Macdonald, Ramsay; Spirig, Thomas; Chan, Albert; Dickson, Claire; Fabian, Marian; Olson, John; Gell, David; Clubb, Robert. "NMR Model of the 38.8 kDa Tri-Domain IsdH Protein from Staphylococcus aureus Suggests that it Adaptively Recognizes Human Hemoglobin"  J. Mol. Biol. 428, 1107-1129 (2016).

Assembly members:
IsdH_N2N3, polymer, 336 residues, 38788.4 Da.

Natural source:   Common Name: firmicutes   Taxonomy ID: 1280   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Staphylococcus aureus

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pRM216

Entity Sequences (FASTA):
IsdH_N2N3: SADESLQDAIKNPAIIDKEH TADNWRPIDFQMKNDKGERQ FYHYASTVEPATVIFTKTGP IIELGLKTASTWKKFEVYEG DKKLPVELVSYDSDKDYAYI RFPVSNGTREVKIVSSIEYG ENIHEDYDYTLMVFAQPITN NPDDYVDEETYNLQKLLAPY HKAKTLERQVYELEKLQEKL PEKYKAEYKKKLDQTRVELA DQVKSAVTEFENVTPTNDQL TDLQEAHFVVFESEENSESV MDGFVEHPFYTATLNGQKYV VMKTKDDSYWKDLIVEGKRV TTVSKDPKNNSRTLIFPYIP DKAVYNAIVKVVVANIGAEG QYHVRIINQDINTKDD

Data sets:
Data typeCount
13C chemical shifts1006
15N chemical shifts292
1H chemical shifts929
T1 relaxation values155
T2 relaxation values142
heteronuclear NOE values238

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1subunits 2-31

Entities:

Entity 1, subunits 2-3 336 residues - 38788.4 Da.

Residue 1 represents a non-native residue left after cleaving of the affinity tag

1   SERALAASPGLUSERLEUGLNASPALAILE
2   LYSASNPROALAILEILEASPLYSGLUHIS
3   THRALAASPASNTRPARGPROILEASPPHE
4   GLNMETLYSASNASPLYSGLYGLUARGGLN
5   PHETYRHISTYRALASERTHRVALGLUPRO
6   ALATHRVALILEPHETHRLYSTHRGLYPRO
7   ILEILEGLULEUGLYLEULYSTHRALASER
8   THRTRPLYSLYSPHEGLUVALTYRGLUGLY
9   ASPLYSLYSLEUPROVALGLULEUVALSER
10   TYRASPSERASPLYSASPTYRALATYRILE
11   ARGPHEPROVALSERASNGLYTHRARGGLU
12   VALLYSILEVALSERSERILEGLUTYRGLY
13   GLUASNILEHISGLUASPTYRASPTYRTHR
14   LEUMETVALPHEALAGLNPROILETHRASN
15   ASNPROASPASPTYRVALASPGLUGLUTHR
16   TYRASNLEUGLNLYSLEULEUALAPROTYR
17   HISLYSALALYSTHRLEUGLUARGGLNVAL
18   TYRGLULEUGLULYSLEUGLNGLULYSLEU
19   PROGLULYSTYRLYSALAGLUTYRLYSLYS
20   LYSLEUASPGLNTHRARGVALGLULEUALA
21   ASPGLNVALLYSSERALAVALTHRGLUPHE
22   GLUASNVALTHRPROTHRASNASPGLNLEU
23   THRASPLEUGLNGLUALAHISPHEVALVAL
24   PHEGLUSERGLUGLUASNSERGLUSERVAL
25   METASPGLYPHEVALGLUHISPROPHETYR
26   THRALATHRLEUASNGLYGLNLYSTYRVAL
27   VALMETLYSTHRLYSASPASPSERTYRTRP
28   LYSASPLEUILEVALGLUGLYLYSARGVAL
29   THRTHRVALSERLYSASPPROLYSASNASN
30   SERARGTHRLEUILEPHEPROTYRILEPRO
31   ASPLYSALAVALTYRASNALAILEVALLYS
32   VALVALVALALAASNILEGLYALAGLUGLY
33   GLNTYRHISVALARGILEILEASNGLNASP
34   ILEASNTHRLYSASPASP

Samples:

sample_1: IsdH N2N3, [U-100% 15N], 1.9 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_2: IsdH N2N3, [U-100% 13C; U-100% 15N], 1.0 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_3: IsdH N2N3, [U-13C; U-15N; U-2H], 1.1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_4: IsdH N2N3, U-[2H], Ile-[13CH3 D1], Leu, Val-[13CH3,12CD3], 0.8 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; D2O 7%; H2O 93%

sample_5: IsdH N2N3, [U-100% 13C; U-100% 15N], 1.2 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; D2O 100%

sample_6: IsdH N2N3, [U-13C; U-15N; U-2H], 1.1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; POLYETHYLENE GLYCOL/HEXANOL 5%; D2O 7%; H2O 93%

sample_7: IsdH N2N3, [U-15N], 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.01%; pf1 PHAGES 9 mg/mL; D2O 7%; H2O 93%

sample_conditions_1: ionic strength: 140 mM; pH: 6.0; pressure: 1 atm; temperature: 310 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_3isotropicsample_conditions_1
2D 1H-15N HSQCsample_4isotropicsample_conditions_1
2D 1H-13C HSQCsample_5isotropicsample_conditions_1
2D 1H-13C HSQCsample_4isotropicsample_conditions_1
3D HNHAsample_2isotropicsample_conditions_1
3D HNCOsample_3isotropicsample_conditions_1
3D HN(CA)COsample_3isotropicsample_conditions_1
3D HNCACBsample_3isotropicsample_conditions_1
3D HN(CO)CACBsample_3isotropicsample_conditions_1
3D HCCH-COSYsample_5isotropicsample_conditions_1
3D HCCH-TOCSYsample_5isotropicsample_conditions_1
3D (H)CCH-TOCSYsample_5isotropicsample_conditions_1
3D HBHA(CO)NHsample_2isotropicsample_conditions_1
3D CC(CO)NHsample_4isotropicsample_conditions_1
3D 1H-15N NOESYsample_3isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_4isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_5isotropicsample_conditions_1
3D 1H-13C NOESYsample_4isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_6anisotropicsample_conditions_1
2D 1H-15N HSQCsample_7anisotropicsample_conditions_1
2D 1H-15N HSQC NOE with interleaved presat and no satsample_3isotropicsample_conditions_1
2D 1H-15N HSQC T1 relaxationsample_1isotropicsample_conditions_1
2D 1H-15N HSQC T2 relaxationsample_1isotropicsample_conditions_1

Software:

PIPP, Garrett - peak picking

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure solution

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

ProcheckNMR, Laskowski and MacArthur - geometry optimization

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

MODULE, (MODULE)-Dosset, P.; Hus, J-C; Marion, D; Blackledge, M. - data analysis

xwinnmr, Bruker Biospin - collection

SPARKY, Goddard - data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker Avance 500 MHz
  • Bruker Avance 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

GB AAW38309.1

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