BMRB Entry 15913
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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/BMR15913
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Title: Solution Structure of the IsdC NEAT domain bound to Zinc Protoporphyrin PubMed: 18715872
Deposition date: 2008-08-07 Original release date: 2008-08-14
Authors: Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert
Citation: Villareal, Valerie; Pilpa, Rosemarie; Robson, Scott; Fadeev, Evgeny; Clubb, Robert. "The IsdC protein from Staphylococcus aureus uses a flexible binding pocket to capture heme" J. Biol. Chem. 283, 31591-31600 (2008).
Assembly members:
IsdC, polymer, 147 residues, 14322.988 Da.
ZNH, non-polymer, 626.051 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):
IsdC: MGSSHHHHHHSSGLVPRGSH
MSANAADSGTLNYEVYKYNT
NDTSIANDYFNKPAKYIKKN
GKLYVQITVNHSHWITGMSI
EGHKENIISKNTAKDERTSE
FEVSKLNGKIDGKIDVYIDE
KVNGKPFKYDHHYNITYKFN
GPTDVAG
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 488 |
| 15N chemical shifts | 130 |
| 1H chemical shifts | 730 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | IsdC | 1 |
| 2 | ZNH | 2 |
Entities:
Entity 1, IsdC 147 residues - 14322.988 Da.
Residues 4-24 represent a Histidine-tag that was not included in the structure calculations
| 1 | MET | GLY | SER | SER | HIS | HIS | HIS | HIS | HIS | HIS | ||||
| 2 | SER | SER | GLY | LEU | VAL | PRO | ARG | GLY | SER | HIS | ||||
| 3 | MET | SER | ALA | ASN | ALA | ALA | ASP | SER | GLY | THR | ||||
| 4 | LEU | ASN | TYR | GLU | VAL | TYR | LYS | TYR | ASN | THR | ||||
| 5 | ASN | ASP | THR | SER | ILE | ALA | ASN | ASP | TYR | PHE | ||||
| 6 | ASN | LYS | PRO | ALA | LYS | TYR | ILE | LYS | LYS | ASN | ||||
| 7 | GLY | LYS | LEU | TYR | VAL | GLN | ILE | THR | VAL | ASN | ||||
| 8 | HIS | SER | HIS | TRP | ILE | THR | GLY | MET | SER | ILE | ||||
| 9 | GLU | GLY | HIS | LYS | GLU | ASN | ILE | ILE | SER | LYS | ||||
| 10 | ASN | THR | ALA | LYS | ASP | GLU | ARG | THR | SER | GLU | ||||
| 11 | PHE | GLU | VAL | SER | LYS | LEU | ASN | GLY | LYS | ILE | ||||
| 12 | ASP | GLY | LYS | ILE | ASP | VAL | TYR | ILE | ASP | GLU | ||||
| 13 | LYS | VAL | ASN | GLY | LYS | PRO | PHE | LYS | TYR | ASP | ||||
| 14 | HIS | HIS | TYR | ASN | ILE | THR | TYR | LYS | PHE | ASN | ||||
| 15 | GLY | PRO | THR | ASP | VAL | ALA | GLY |
Entity 2, ZNH - C34 H32 N4 O4 Zn - 626.051 Da.
| 1 | ZNH |
Samples:
sample_1: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC, [U-100% 13C; U-100% 15N], 1.3 mM; ZNH 2.1 mM; D2O, [U-100% 2H], 7%; H2O 93%
sample_2: sodium phosphate 50 mM; sodium chloride 100 mM; sodium azide 0.01%; IsdC 1.1 mM; ZNH 2.3 mM; D2O 100%
sample_conditions_1: ionic strength: 150 mM; pH: 6; pressure: 1 atm; temperature: 302 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_2 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHA | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-COSY | sample_2 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNHB | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
PIPP, Garrett - peak picking
NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
ATHNOS-CANDID, Herrmann, Guntert, Wuthrich - chemical shift assignment
CARA, Keller - chemical shift assignment
NMR spectrometers:
- Bruker Avance 500 MHz
- Bruker Avance 600 MHz
- Bruker Avance 800 MHz
Related Database Links:
| PDB | |
| DBJ | BAB42227 BAB57293 BAB94878 BAF67314 BAF78005 |
| EMBL | CAG40106 CAG42839 CAI80683 CAQ49552 CBI49004 |
| GB | AAL33767 AAW38020 ABD20415 ABD30198 ABQ48990 |
| REF | WP_000789795 WP_000789808 WP_000789809 WP_000789810 WP_000789811 |
| SP | A5IS17 A6QG32 A6U0U8 A7X149 A8Z1R1 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts