BMRB Entry 16145
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16145
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Title: Structure of SDF-1/CXCL12 PubMed: 19551879
Deposition date: 2009-01-28 Original release date: 2009-06-25
Authors: Volkman, B.; Veldkamp, C.; Peterson, F.
Citation: Veldkamp, C.; Ziarek, J.; Su, J.; Basnet, H.; Lennertz, R.; Weiner, J.; Peterson, F.; Baker, J.; Volkman, B.. "Monomeric structure of the cardioprotective chemokine SDF-1/CXCL12" Protein Sci. 18, 1359-1369 (2009).
Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8122.656 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: Escherichia coli
Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GSKPVSLSYRCPCRFFESHV
ARANVKHLKILNTPNCALQI
VARLKNNNRQVCIDPKLKWI
QEYLEKALNK
- assigned_chemical_shifts
| Data type | Count |
| 13C chemical shifts | 319 |
| 15N chemical shifts | 76 |
| 1H chemical shifts | 528 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CXCL12/SDF1-alpha | 1 |
Entities:
Entity 1, CXCL12/SDF1-alpha 70 residues - 8122.656 Da.
| 1 | GLY | SER | LYS | PRO | VAL | SER | LEU | SER | TYR | ARG | |
| 2 | CYS | PRO | CYS | ARG | PHE | PHE | GLU | SER | HIS | VAL | |
| 3 | ALA | ARG | ALA | ASN | VAL | LYS | HIS | LEU | LYS | ILE | |
| 4 | LEU | ASN | THR | PRO | ASN | CYS | ALA | LEU | GLN | ILE | |
| 5 | VAL | ALA | ARG | LEU | LYS | ASN | ASN | ASN | ARG | GLN | |
| 6 | VAL | CYS | ILE | ASP | PRO | LYS | LEU | LYS | TRP | ILE | |
| 7 | GLN | GLU | TYR | LEU | GLU | LYS | ALA | LEU | ASN | LYS |
Samples:
sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], 1.2 mM; H2O 90%; D2O 10%; MES 20 mM
sample_conditions_1: ionic strength: 0.001 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 3D_15N-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D_13C-separated_NOESY (AROMATIC) | sample_1 | isotropic | sample_conditions_1 |
Software:
X-PLOR NIH v2.9.3, Schwieters, Kuszewski, Tjandra and Clore - refinement
TOPSPIN, Bruker Biospin - collection
NMRPipe v2004, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing
XEASY v1.3, Bartels et al. - data analysis
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
NMR spectrometers:
- Bruker DRX 600 MHz
Related Database Links:
| BMRB | 16142 16143 16519 |
| PDB | |
| DBJ | BAA28601 BAA28602 BAF85317 BAG11056 BAG34757 |
| EMBL | CAE11785 CAG29279 |
| GB | AAA97434 AAB39332 AAB39333 AAB40516 AAH39893 |
| REF | NP_000600 NP_001009580 NP_001009847 NP_001012495 NP_001028106 |
| SP | O62657 P48061 |
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