BMRB Entry 15271
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR15271
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Title: Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris PubMed: 17766387
Deposition date: 2007-05-30 Original release date: 2007-12-19
Authors: Kjaergaard, Magnus; Gaardsvoll, Henrik; Hirschberg, Daniel; Nielbo, Steen; Mayasundari, Anand; Peterson, Cynthia; Jansson, Anna; Jorgensen, Thomas; Poulsen, Flemming; Ploug, Michael
Citation: Kjaergaard, Magnus; Gaardsvoll, Henrik; Hirschberg, Daniel; Nielbo, Steen; Mayasundari, Anand; Peterson, Cynthia; Jansson, Anna; Jorgensen, Thomas; Poulsen, Flemming; Ploug, Michael. "Solution structure of recombinant Somatomedin B domain from vitronectin produced in Pichia pastoris" Protein Sci. 16, 1934-1945 (2007).
Assembly members:
SMB, polymer, 53 residues, 5346.906 Da.
Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens
Experimental source: Production method: recombinant technology Host organism: Pichia pastoris
Entity Sequences (FASTA):
SMB: DQESCKGRCTEGFNVDKKCQ
CDELCSYYQSCCTDYTAECK
PQVTRGDHHHHHH
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 166 |
| 15N chemical shifts | 44 |
| 1H chemical shifts | 270 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | Somatomedin B | 1 |
Entities:
Entity 1, Somatomedin B 53 residues - 5346.906 Da.
| 1 | ASP | GLN | GLU | SER | CYS | LYS | GLY | ARG | CYS | THR | ||||
| 2 | GLU | GLY | PHE | ASN | VAL | ASP | LYS | LYS | CYS | GLN | ||||
| 3 | CYS | ASP | GLU | LEU | CYS | SER | TYR | TYR | GLN | SER | ||||
| 4 | CYS | CYS | THR | ASP | TYR | THR | ALA | GLU | CYS | LYS | ||||
| 5 | PRO | GLN | VAL | THR | ARG | GLY | ASP | HIS | HIS | HIS | ||||
| 6 | HIS | HIS | HIS |
Samples:
sample_1: SMB, [U-99% 13C; U-99% 15N], 0.4 mM
sample_2: SMB 0.7 mM; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 0 M; pH: 6.5; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCA | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACB | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(CO)CA | sample_1 | isotropic | sample_conditions_1 |
| 3D HN(COCA)CB | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-1H NOESY | sample_2 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | sample_1 | isotropic | sample_conditions_1 |
Software:
PRONTO, Kj r, Andersen and Poulsen - chemical shift assignment
NMRDraw, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
SPARKY, Goddard - data analysis
CYANA, Guntert, Mumenthaler and Wuthrich - structure solution
CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
NMR spectrometers:
- Varian Unity 750 MHz
Related Database Links:
| PDB | |
| DBJ | BAG35807 BAI47214 |
| EMBL | CAA26933 CAA28659 CAI29588 |
| GB | AAH05046 AAK60270 ABM84320 ABM87715 ADL14521 |
| REF | NP_000629 NP_001127063 XP_001106884 XP_001146856 XP_003912541 |
| SP | P04004 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts