BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 16807

Title: Solution NMR Structure of the Holo Form of a Ribonuclease H domain from D.hafniense, Northeast Structural Genomics Consortium Target Target DhR1A

Deposition date: 2010-03-31 Original release date: 2010-04-14

Authors: Mills, J.; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.

Citation: Mills, Jeffrey; Eletsky, A.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, T.. "Northeast Structural Genomics Consortium Target DhR1A"  To be published ., .-..

Assembly members:
DhR1A, polymer, 147 residues, 16699.068 Da.
MG, non-polymer, 24.305 Da.

Natural source:   Common Name: Desulfitobacterium hafniense   Taxonomy ID: 49338   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Desulfitobacterium hafniense

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

Entity Sequences (FASTA):
DhR1A: MDDRTEYDVYTDGSYVNGQY AWAYAFVKDGKVHYEDADVG KNPAAATMRNVAGEIAAALY AVKKASQLGVKIRILHDYAG IAFWATGEWKAKNEFTQAYA KLMNQYRGIYSFEKVKAHSG NEFNDYVDMKAKSALGIRDL EHHHHHH

Data sets:
Data typeCount
13C chemical shifts372
15N chemical shifts134
1H chemical shifts821

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1DhR1A1
2Magnesium ion2

Entities:

Entity 1, DhR1A 147 residues - 16699.068 Da.

1   METASPASPARGTHRGLUTYRASPVALTYR
2   THRASPGLYSERTYRVALASNGLYGLNTYR
3   ALATRPALATYRALAPHEVALLYSASPGLY
4   LYSVALHISTYRGLUASPALAASPVALGLY
5   LYSASNPROALAALAALATHRMETARGASN
6   VALALAGLYGLUILEALAALAALALEUTYR
7   ALAVALLYSLYSALASERGLNLEUGLYVAL
8   LYSILEARGILELEUHISASPTYRALAGLY
9   ILEALAPHETRPALATHRGLYGLUTRPLYS
10   ALALYSASNGLUPHETHRGLNALATYRALA
11   LYSLEUMETASNGLNTYRARGGLYILETYR
12   SERPHEGLULYSVALLYSALAHISSERGLY
13   ASNGLUPHEASNASPTYRVALASPMETLYS
14   ALALYSSERALALEUGLYILEARGASPLEU
15   GLUHISHISHISHISHISHIS

Entity 2, Magnesium ion - Mg - 24.305 Da.

1   MG

Samples:

sample: DhR1A, [U-100% 13C; U-100% 15N], 0.89 mM; MAGNESIUM Chloride 150 mM; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02%; H2O 95%; D2O 5%

sample_conditions_1: pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsampleisotropicsample_conditions_1
2D 1H-13C HSQCsampleisotropicsample_conditions_1
3D HNCOsampleisotropicsample_conditions_1
3D CBCA(CO)NHsampleisotropicsample_conditions_1
3D HNCACBsampleisotropicsample_conditions_1
3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESYsampleisotropicsample_conditions_1
3D HBHA(CO)NHsampleisotropicsample_conditions_1
3D HCCH-TOCSYsampleisotropicsample_conditions_1

Software:

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - geometry optimization, refinement, structure solution

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

XEASY, Bartels et al. - chemical shift assignment, data analysis, peak picking

TOPSPIN, Bruker Biospin - collection

VNMRJ, Varian - collection

CARA, Keller and Wuthrich - chemical shift assignment

Molmol, Koradi, Billeter and Wuthrich - refinement

TALOS, Cornilescu, Delaglio and Bax - geometry optimization

NMR spectrometers:

  • Bruker Avance 900 MHz
  • Varian INOVA 750 MHz

Related Database Links:

BMRB 16578
PDB
DBJ BAE83579
EMBL CDX01853
GB ACL20967 EHL06967
REF WP_005812143 WP_018211583 WP_019850577

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