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Biological Magnetic Resonance Data Bank


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BMRB Entry 17643

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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/BMR17643
MolProbity Validation Chart

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Title: Backbone 1H, 13C, and 15N Chemical Shift Assignments for full-length YtvA from Bacillus subtilis   PubMed: 21851109

Deposition date: 2011-05-13 Original release date: 2011-08-12

Authors: Jurk, Marcel; Schmieder, Peter

Citation: Jurk, Marcel; Dorn, Matthias; Schmieder, Peter. "Blue flickers of hope: secondary structure, dynamics, and putative dimerization interface of the blue-light receptor YtvA from Bacillus subtilis."  Biochemistry 50, 8163-8171 (2011).

Assembly members:
YtvA, polymer, 261 residues, 29500 Da.
FMN, non-polymer, 456.344 Da.

Natural source:   Common Name: Bacillus subtilis   Taxonomy ID: 1423   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Bacillus subtilis

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

Entity Sequences (FASTA):
YtvA: GASFQSFGIPGQLEVIKKAL DHVRVGVVITDPALEDNPIV YVNQGFVQMTGYETEEILGK NCRFLQGKHTDPAEVDNIRT ALQNKEPVTVQIQNYKKDGT MFWNELNIDPMEIEDKTYFV GIQNDITKQKEYEKLLEDSL TEITALSTPIVPIRNGISAL PLVGNLTEERFNSIVCTLTN ILSTSKDDYLIIDLSGLAQV NEQTADQIFKLSHLLKLTGT ELIITGIKPELAMKMNKLDA NFSSLKTYSNVKDAVKVLPI M

Data sets:
Data typeCount
13C chemical shifts782
15N chemical shifts242
1H chemical shifts347

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1Monomer 11
2Monomer 21
3Cofactor 12
4Cofactor 22

Entities:

Entity 1, Monomer 1 261 residues - 29500 Da.

Gly1 is a remainder of the proteolytic cleavage site

1   GLYALASERPHEGLNSERPHEGLYILEPRO
2   GLYGLNLEUGLUVALILELYSLYSALALEU
3   ASPHISVALARGVALGLYVALVALILETHR
4   ASPPROALALEUGLUASPASNPROILEVAL
5   TYRVALASNGLNGLYPHEVALGLNMETTHR
6   GLYTYRGLUTHRGLUGLUILELEUGLYLYS
7   ASNCYSARGPHELEUGLNGLYLYSHISTHR
8   ASPPROALAGLUVALASPASNILEARGTHR
9   ALALEUGLNASNLYSGLUPROVALTHRVAL
10   GLNILEGLNASNTYRLYSLYSASPGLYTHR
11   METPHETRPASNGLULEUASNILEASPPRO
12   METGLUILEGLUASPLYSTHRTYRPHEVAL
13   GLYILEGLNASNASPILETHRLYSGLNLYS
14   GLUTYRGLULYSLEULEUGLUASPSERLEU
15   THRGLUILETHRALALEUSERTHRPROILE
16   VALPROILEARGASNGLYILESERALALEU
17   PROLEUVALGLYASNLEUTHRGLUGLUARG
18   PHEASNSERILEVALCYSTHRLEUTHRASN
19   ILELEUSERTHRSERLYSASPASPTYRLEU
20   ILEILEASPLEUSERGLYLEUALAGLNVAL
21   ASNGLUGLNTHRALAASPGLNILEPHELYS
22   LEUSERHISLEULEULYSLEUTHRGLYTHR
23   GLULEUILEILETHRGLYILELYSPROGLU
24   LEUALAMETLYSMETASNLYSLEUASPALA
25   ASNPHESERSERLEULYSTHRTYRSERASN
26   VALLYSASPALAVALLYSVALLEUPROILE
27   MET

Entity 2, Cofactor 1 - C17 H21 N4 O9 P - 456.344 Da.

1   FMN

Samples:

sample_1: YtvA, [U-13C; U-15N; U-2H], 500 ± 0.1 uM; potassium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.1%; H20 95%; D20 5%; FMN, [U-75% 13C; U-75% 15N; U-75% 2H], 500 uM

sample_2: YtvA, [U-15N; U-2H], 500 uM; potassium phosphate 20 mM; sodium chloride 50 mM; sodium azide 0.1%; H20 95%; D20 5%; FMN, [U-75% 15N; U-75% 2H], 500 uM

sample_conditions_1: ionic strength: 70 mM; pH: 6.5; pressure: 1 atm; temperature: 300 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N TROSYsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D HNCA(NH)sample_1isotropicsample_conditions_1
2D 1H-15N TROSYsample_2isotropicsample_conditions_1

Software:

TOPSPIN v2.1, Bruker Biospin - collection, processing

CCPN v2.1.5, Vranken et al. - chemical shift assignment, data analysis, peak picking

NMR spectrometers:

  • Bruker Avance 600 MHz

Related Database Links:

DBJ BAI86545 BAM54284 BAM59113 GAK82103
EMBL CAB15012 CCU59545 CEI58264 CEJ78686 CJR42913
GB AAC00382 ABN71355 ACR16779 ACR43777 ADJ00051
REF NP_390912 WP_003229169 WP_004399022 WP_014477717 WP_014480616
SP O34627

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