BMRB Entry 30820

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR30820
MolProbity Validation Chart

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Title:
NMR Structure of a tRNA 2'-phosphotransferase from Runella slithyformis in complex with NAD+
Deposition date:
2020-11-30
Original release date:
2021-10-08
Authors:
Alphonse, S.; Dantuluri, S.; Banerjee, A.; Shuman, S.; Ghose, R.
Citation:

Citation: Alphonse, Sebastien; Banerjee, Ankan; Dantuluri, Swathi; Shuman, Stewart; Ghose, Ranajeet. "NMR solution structures of Runella slithyformis RNA 2'-phosphotransferase Tpt1 provide insights into NAD+ binding and specificity"  Nucleic Acids Res. 49, 9607-9624 (2021).
PubMed: 33880546

Assembly members:

Assembly members:
entity_1, polymer, 178 residues, 19846.059 Da.
entity_NAD, non-polymer, 663.425 Da.

Natural source:

Natural source:   Common Name: Runella slithyformis   Taxonomy ID: 106   Superkingdom: Bacteria   Kingdom: not available   Genus/species: Runella slithyformis

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSHMVKVSKFLSLVLRHNPA LIGLDLDANGWAPVKELLAK MKAKGHGISMEELKHIVETN SKKRFAFSENFEKIRANQGH SVEVDLGYEKQVPPAVLFHG TAEKNFDLILKDGIKKMSRH HVHLSQDITTARKVGMRHGK PVVLSVDAKGMADGGFDFYL SNNGVWLIDFVPAEFIKV

Data sets:
Data typeCount
13C chemical shifts703
15N chemical shifts172
1H chemical shifts1111

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 178 residues - 19846.059 Da.

1   GLYSERHISMETVALLYSVALSERLYSPHE
2   LEUSERLEUVALLEUARGHISASNPROALA
3   LEUILEGLYLEUASPLEUASPALAASNGLY
4   TRPALAPROVALLYSGLULEULEUALALYS
5   METLYSALALYSGLYHISGLYILESERMET
6   GLUGLULEULYSHISILEVALGLUTHRASN
7   SERLYSLYSARGPHEALAPHESERGLUASN
8   PHEGLULYSILEARGALAASNGLNGLYHIS
9   SERVALGLUVALASPLEUGLYTYRGLULYS
10   GLNVALPROPROALAVALLEUPHEHISGLY
11   THRALAGLULYSASNPHEASPLEUILELEU
12   LYSASPGLYILELYSLYSMETSERARGHIS
13   HISVALHISLEUSERGLNASPILETHRTHR
14   ALAARGLYSVALGLYMETARGHISGLYLYS
15   PROVALVALLEUSERVALASPALALYSGLY
16   METALAASPGLYGLYPHEASPPHETYRLEU
17   SERASNASNGLYVALTRPLEUILEASPPHE
18   VALPROALAGLUPHEILELYSVAL

Entity 2, unit_2 - C21 H27 N7 O14 P2 - 663.425 Da.

1   NAD

Samples:

sample_1: Tpt1, [U-13C; U-15N], 600 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2.4 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_2: Tpt1, [U-13C; U-15N], 280 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1.12 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_3: Tpt1, [U-13C; U-15N], 325 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1.3 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_4: Tpt1, [U-13C; U-15N], 300 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1.2 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_5: Tpt1, [U-13C; U-15N; U-2H], 500 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 2 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_6: Tpt1, [U-13C; U-15N], 400 uM; NICOTINAMIDE-ADENINE-DINUCLEOTIDE 1.6 mM; HEPES 20 mM; sodium chloride 200 mM; DTT 2 mM; EDTA, [U-2H], 2 mM; glycerol, [U-2H], 5 % v/v; AEBSF protease inhibitor 1 mM; sodium azide 0.04 % w/v; DSS 50 uM

sample_conditions_1: pH: 7; pressure: 1 atm; temperature: 290.15 K

sample_conditions_2: pH: 7 pH*; pressure: 1 atm; temperature: 290.15 K

Experiments:

NameSampleSample stateSample conditions
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCAsample_2isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_3isotropicsample_conditions_2
3D HCCH-TOCSYsample_3isotropicsample_conditions_2
2D 1H-1H NOESYsample_4isotropicsample_conditions_2
3D 1H-15N NOESYsample_5isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_3isotropicsample_conditions_2
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_3isotropicsample_conditions_2
3D 1H-13C NOESY methylsample_4isotropicsample_conditions_2
4D 1H-13C-13C-1H NOESY methylsample_6isotropicsample_conditions_2

Software:

NMRPipe v10.3 Revision 2019.220.13.40, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

TopSpin v3.5p15, Bruker Biospin - collection

NMRView, Johnson, One Moon Scientific - chemical shift assignment

ARIA v2.3.2, Linge, O'Donoghue and Nilges - structure calculation

X-PLOR NIH v2.52, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

  • Bruker AVANCE III HD 600 MHz
  • Bruker AVANCE III HD 700 MHz
  • Bruker AVANCE III HD 800 MHz
  • Bruker AVANCE III HD 800 MHz
  • Bruker AVANCE III 700 MHz
  • Bruker AVANCE II 900 MHz

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