BMRB Entry 17862
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: LACS
BMRB Entry DOI: doi:10.13018/BMR17862
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Title: Solution structure of Staphylococcus aureus IsdH linker domain PubMed: 21917915
Deposition date: 2011-08-12 Original release date: 2012-06-19
Authors: Spirig, Thomas; Clubb, Robert; Malmirchegini, G.; Robson, Scott
Citation: Krishna Kumar, Kaavya; Jacques, David; Pishchany, Gleb; Caradoc-Davies, Tom; Spirig, Thomas; Malmirchegini, G. Reza; Langley, David; Dickson, Claire; Mackay, Joel; Clubb, Robert; Skaar, Eric; Guss, J. Mitchell; Gell, David. "Structural basis for hemoglobin capture by Staphylococcus aureus cell-surface protein, IsdH." J. Biol. Chem. 286, 38439-38447 (2011).
Assembly members:
entity, polymer, 78 residues, 9280.425 Da.
Natural source: Common Name: Staphylococcus aureus Taxonomy ID: 1280 Superkingdom: Bacteria Kingdom: not available Genus/species: Staphylococcus aureus
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
entity: SDDYVDEETYNLQKLLAPYH
KAKTLERQVYELEKLQEKLP
EKYKAEYKKKLDQTRVELAD
QVKSAVTEFENVTPTNDQ
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 357 |
| 15N chemical shifts | 82 |
| 1H chemical shifts | 568 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Staphylococcus aureus IsdH linker domain | 1 |
Entities:
Entity 1, Staphylococcus aureus IsdH linker domain 78 residues - 9280.425 Da.
Residue 1 represents a non-native residue left after cleaving of the affinity tag
| 1 | SER | ASP | ASP | TYR | VAL | ASP | GLU | GLU | THR | TYR | ||||
| 2 | ASN | LEU | GLN | LYS | LEU | LEU | ALA | PRO | TYR | HIS | ||||
| 3 | LYS | ALA | LYS | THR | LEU | GLU | ARG | GLN | VAL | TYR | ||||
| 4 | GLU | LEU | GLU | LYS | LEU | GLN | GLU | LYS | LEU | PRO | ||||
| 5 | GLU | LYS | TYR | LYS | ALA | GLU | TYR | LYS | LYS | LYS | ||||
| 6 | LEU | ASP | GLN | THR | ARG | VAL | GLU | LEU | ALA | ASP | ||||
| 7 | GLN | VAL | LYS | SER | ALA | VAL | THR | GLU | PHE | GLU | ||||
| 8 | ASN | VAL | THR | PRO | THR | ASN | ASP | GLN |
Samples:
sample_1: IsdH linker, [U-100% 15N], 1.1 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 7%; H2O 93%
sample_2: IsdH linker, [U-100% 13C; U-100% 15N], 1.3 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 7%; H2O 93%
sample_3: IsdH linker, [U-100% 13C; U-100% 15N], 1.3 mM; potassium phosphate 20 mM; potassium chloride 50 mM; AEBSF protease inhibitor 100 uM; sodium azide 0.01%; D2O 100%
sample_conditions_1: ionic strength: 140 mM; 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 HNCACB | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HN(CA)CO | sample_2 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_2 | isotropic | sample_conditions_1 |
| 3D CC(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_2 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHB | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_3 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_3 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY aromatic | sample_3 | isotropic | sample_conditions_1 |
| 2D CB(CGCD)HD | sample_3 | isotropic | sample_conditions_1 |
| 2D CB(CGCD)HE | sample_3 | isotropic | sample_conditions_1 |
Software:
PIPP, Garrett - peak picking
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
UNIO, Herrmann, Guntert and Wuthrich - chemical shift assignment
ProcheckNMR, Laskowski and MacArthur - geometry optimization
TALOS, Cornilescu, Delaglio and Bax - geometry optimization
xwinnmr, Bruker Biospin - collection
CARA, Keller - chemical shift assignment
NMR spectrometers:
- Bruker Avance 500 MHz
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
| BMRB | 17820 |
| PDB | |
| DBJ | BAB42820 BAB57893 BAB95538 BAF67896 BAF78600 |
| EMBL | CAG43459 CAI81279 CAQ50207 CBI49597 CBX34951 |
| GB | AAW38309 ABD20516 ABD30910 ABQ49576 ABR52665 |
| REF | WP_001032759 WP_001032760 WP_001032761 WP_001032762 WP_001032763 |
| SP | Q2FG07 Q2FXJ2 Q2YTF7 Q5HF43 Q6G8J7 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts