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
MolProbity Validation Chart

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Title:
Solution structure of the Somatomedin B domain from vitronectin produced in Pichia pastoris
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:

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).
PubMed: 17766387

Assembly members:

Assembly members:
SMB, polymer, 53 residues, 5346.906 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: Pichia pastoris   Vector: pPICZalpha A

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SMB: DQESCKGRCTEGFNVDKKCQ CDELCSYYQSCCTDYTAECK PQVTRGDHHHHHH

Data sets:
Data typeCount
13C chemical shifts166
15N chemical shifts44
1H chemical shifts270

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Somatomedin B1

Entities:

Entity 1, Somatomedin B 53 residues - 5346.906 Da.

1   ASPGLNGLUSERCYSLYSGLYARGCYSTHR
2   GLUGLYPHEASNVALASPLYSLYSCYSGLN
3   CYSASPGLULEUCYSSERTYRTYRGLNSER
4   CYSCYSTHRASPTYRTHRALAGLUCYSLYS
5   PROGLNVALTHRARGGLYASPHISHISHIS
6   HISHISHIS

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:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(COCA)CBsample_1isotropicsample_conditions_1
2D 1H-1H NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-15N TOCSYsample_1isotropicsample_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
AlphaFold P04004

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