BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 19811

Title: NMR solution structure of a computational designed protein based on template of human erythrocytic ubiquitin

Deposition date: 2014-02-21 Original release date: 2014-10-27

Authors: Xiong, Peng; Wang, Meng; Zhang, Jiahai; Chen, Quan; Liu, Haiyan

Citation: Xiong, Peng; Wang, Meng; Zhou, Xiaoqun; Zhang, Tongchuan; Zhang, Jiahai; Chen, Quan; Liu, Haiyan. "A comprehensive statistical energy function for protein design"  Nat. Methods ., .-..

Assembly members:
redesigned_ubiquitin, polymer, 79 residues, 8559.913 Da.

Natural source:   Common Name: not available   Taxonomy ID: not available   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

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

Entity Sequences (FASTA):
redesigned_ubiquitin: MDTINITLPDGKTLTLTVTP EFTVKELAEEIARRLGLSPE DIKLTHNGKTLDPSLTLAEY GITPGSTITLEIKKKGGLE

Data sets:
Data typeCount
13C chemical shifts264
15N chemical shifts76
1H chemical shifts561

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1redesigned ubiquitin1

Entities:

Entity 1, redesigned ubiquitin 79 residues - 8559.913 Da.

1   METASPTHRILEASNILETHRLEUPROASP
2   GLYLYSTHRLEUTHRLEUTHRVALTHRPRO
3   GLUPHETHRVALLYSGLULEUALAGLUGLU
4   ILEALAARGARGLEUGLYLEUSERPROGLU
5   ASPILELYSLEUTHRHISASNGLYLYSTHR
6   LEUASPPROSERLEUTHRLEUALAGLUTYR
7   GLYILETHRPROGLYSERTHRILETHRLEU
8   GLUILELYSLYSLYSGLYGLYLEUGLU

Samples:

sample_1: redesigned ubiquitin, [U-100% 15N], 0.5 – 1 mM; phosphate buffer 25 mM; sodium chloride 100 mM; EDTA 2 mM; D2O, [U-100% 2H], 10%; H2O 90%

sample_2: redesigned ubiquitin, [U-100% 13C], 0.5 – 1 mM; phosphate buffer 25 mM; sodium chloride 100 mM; EDTA 2 mM; D2O, [U-100% 2H], 100%

sample_conditions_1: ionic strength: 125 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1

Software:

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - geometry optimization, refinement, structure solution

NMR spectrometers:

  • Bruker DMX 600 MHz

Related Database Links:

PDB

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts