BMRB Entry 16142

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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/BMR16142
MolProbity Validation Chart

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Title:
Structure of SDF-1/CXCL12
Deposition date:
2009-01-28
Original release date:
2009-06-25
Authors:
Volkman, B.; Veldkamp, C.; Peterson, F.
Citation:

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).
PubMed: 19551879

Assembly members:

Assembly members:
CXCL12/SDF1-alpha, polymer, 70 residues, 8166.771 Da.

Natural source:

Natural source:   Common Name: Human   Taxonomy ID: 9606   Superkingdom: Eukaryota   Kingdom: Metazoa   Genus/species: Homo sapiens

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: PQE30

Entity Sequences (FASTA):

Entity Sequences (FASTA):
CXCL12/SDF1-alpha: GMKPVSLSYRCPCRFFESHV ARANVKHLKILNTPNCALQI VARLKNNNRQVCIDPKLKWI QEYLEKALNK

Data sets:
Data typeCount
13C chemical shifts319
15N chemical shifts76
1H chemical shifts528

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1CXCL12/SDF1-alpha1

Entities:

Entity 1, CXCL12/SDF1-alpha 70 residues - 8166.771 Da.

1   GLYMETLYSPROVALSERLEUSERTYRARG
2   CYSPROCYSARGPHEPHEGLUSERHISVAL
3   ALAARGALAASNVALLYSHISLEULYSILE
4   LEUASNTHRPROASNCYSALALEUGLNILE
5   VALALAARGLEULYSASNASNASNARGGLN
6   VALCYSILEASPPROLYSLEULYSTRPILE
7   GLNGLUTYRLEUGLULYSALALEUASNLYS

Samples:

sample_1: CXCL12/SDF1-alpha, [U-100% 13C; U-100% 15N], 1.56 mM; H2O 90%; D2O 10%; sodium phosphate 50 mM; MES 20 mM

sample_conditions_1: ionic strength: 50 mM; pH: 5.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
3D_15N-separated_NOESYsample_1isotropicsample_conditions_1
3D_13C-separated_NOESYsample_1isotropicsample_conditions_1
3D_13C-separated_NOESY (AROMATIC)sample_1isotropicsample_conditions_1

Software:

X-PLOR NIH v2.9.3, SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJANDRA,N.,CLORE,G.M. - refinement

xwinnmr v3.5, Bruker - collection

NMRPipe v2004, Delagio,F. et al. - processing

XEASY v1.3, Eccles, C., Guntert, P., Billeter, M., Wuthrich, K. - data analysis

GARANT v2.1, C. Bartels - data analysis

CYANA v2.1, Guntert, P. - structural calculation

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

BMRB 15633 15635 15636 15637 16143 16145 16519
PDB
DBJ BAA04648 BAA07862 BAA07863 BAA28601 BAA28602
EMBL CAE11785 CAG29279 CAH91884 CAJ18596
GB AAA40100 AAA40101 AAA97434 AAB32650 AAB39332
PIR I53416
REF NP_000600 NP_001009580 NP_001009847 NP_001012495 NP_001028106
SP O62657 P40224 P48061
AlphaFold O62657 P40224 P48061

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