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Biological Magnetic Resonance Data Bank


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BMRB Entry 16578

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR16578
MolProbity Validation Chart

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Title: Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A.

Deposition date: 2009-10-24 Original release date: 2012-08-03

Authors: Mills, Jeffrey; Eletsky, Alexander; Hua, Jia; Belote, Rachel; Buchwald, William; Ciccosanti, Colleen; Janjua, Haleema; Nair, R.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, Thomas

Citation: Mills, Jeffrey; Eletsky, Alexander; Hua, Jia; Belote, Rachel; Buchwald, William; Ciccosanti, Colleen; Janjua, Haleema; Nair, R.; Rost, B.; Acton, T.; Xiao, R.; Everett, J.; Montelione, G.; Szyperski, Thomas. "Solution NMR structure of the apo form of a ribonuclease H domain of protein DSY1790 from Desulfitobacterium hafniense, Northeast Structural Genomics target DhR1A."  Not known ., .-..

Assembly members:
DSY1790, polymer, 147 residues, 16692.779 Da.

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

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

Entity Sequences (FASTA):
DSY1790: MDDRTEYDVYTDGSYVNGQY AWAYAFVKDGKVHYEDADVG KNPAAATMRNVAGEIAAALY AVKKASQLGVKIRILHDYAG IAFWATGEWKAKNEFTQAYA KLMNQYRGIYSFEKVKAHSG NEFNDYVDMKAKSALGIRDL EHHHHHH

Data sets:
Data typeCount
13C chemical shifts394
15N chemical shifts132
1H chemical shifts838

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1DSY17901

Entities:

Entity 1, DSY1790 147 residues - 16692.779 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

Samples:

NC: DhR1A, [U-99% 13C; U-99% 15N], 0.89 mM; D2O, [U-2H], 10 v/v; H2O 90 v/v; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02 w/v

NC5: DhR1A, [U-5% 13C; U-99% 15N], 0.943 mM; D2O, [U-2H], 10 v/v; H2O 90 v/v; MES 20 mM; sodium chloride 200 mM; calcium chloride 5 mM; DTT 10 mM; DSS 50 uM; sodium azide 0.02 w/v

sample_conditions_1: ionic strength: 430 mM; pH: 6.5; pressure: 1 atm; temperature: 298 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCNCisotropicsample_conditions_1
2D 1H-13C HSQCNCisotropicsample_conditions_1
2D 1H-13C HSQCNC5isotropicsample_conditions_1
3D CBCA(CO)NHNCisotropicsample_conditions_1
3D HNCONCisotropicsample_conditions_1
3D HNCACBNCisotropicsample_conditions_1
3D HBHA(CO)NHNCisotropicsample_conditions_1
3D HCCH-COSYNCisotropicsample_conditions_1
3D simultaneous NOESYNCisotropicsample_conditions_1

Software:

VNMRJ, Varian - collection

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

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

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

SPSCAN, Glaser - processing

AutoAssign, Zimmerman, Moseley, Kulikowski and Montelione - chemical shift assignment

CSI, Wishart and Sykes - structure solution

TALOS, Cornilescu, Delaglio and Bax - structure solution

CYANA, Herrmann, Guntert and Wuthrich - structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

Molmol, Koradi, Billeter and Wuthrich - data analysis, refinement

PSVS, Bhattacharya and Montelione - refinement

NMR spectrometers:

  • Varian UnityPlus 600 MHz
  • Bruker Avance 800 MHz

Related Database Links:

BMRB 16807
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