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Biological Magnetic Resonance Data Bank


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BMRB Entry 25482

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25482
MolProbity Validation Chart

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Title: Solution structural studies of GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) from Methanocaldococcus jannaschii   PubMed: 26513744

Deposition date: 2015-02-11 Original release date: 2015-11-09

Authors: Singarapu, Kiran Kumar; Otte, Michele; Tonelli, Marco; Westler, William; Escalante-Semerena, Jorge; Markley, John

Citation: Singarapu, Kiran Kumar; Otte, Michele; Tonelli, Marco; Westler, William; Escalante-Semerena, Jorge; Markley, John. "Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii"  Plos One 10, e0141297-e0141297 (2015).

Assembly members:
CobY, polymer, 196 residues, 21770.621 Da.

Natural source:   Common Name: euryarchaeotes   Taxonomy ID: 2190   Superkingdom: Archaea   Kingdom: not available   Genus/species: Methanococcus jannaschii

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

Entity Sequences (FASTA):
CobY: MDALIMAGGKGTRMGGVEKP LIKLCGRCLIDYVVSPLLKS KVNNIFIATSPNTPKTKEYI NSAYKDYKNIVVIDTSGKGY IEDLNECIGYFSEPFLVVSS DLINLKSKIINSIVDYFYCI KAKTPDVEALAVMIPKEKYP NPSIDFNGLVPAGINVVSPK HGYQKEEIMVIDELIFNINT KDDLKLAEMLLKKDGL

Data sets:
Data typeCount
13C chemical shifts705
15N chemical shifts156
1H chemical shifts1364

Additional metadata:

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

Entity Assembly IDEntity NameEntity ID
1CobY1

Entities:

Entity 1, CobY 196 residues - 21770.621 Da.

1   METASPALALEUILEMETALAGLYGLYLYS
2   GLYTHRARGMETGLYGLYVALGLULYSPRO
3   LEUILELYSLEUCYSGLYARGCYSLEUILE
4   ASPTYRVALVALSERPROLEULEULYSSER
5   LYSVALASNASNILEPHEILEALATHRSER
6   PROASNTHRPROLYSTHRLYSGLUTYRILE
7   ASNSERALATYRLYSASPTYRLYSASNILE
8   VALVALILEASPTHRSERGLYLYSGLYTYR
9   ILEGLUASPLEUASNGLUCYSILEGLYTYR
10   PHESERGLUPROPHELEUVALVALSERSER
11   ASPLEUILEASNLEULYSSERLYSILEILE
12   ASNSERILEVALASPTYRPHETYRCYSILE
13   LYSALALYSTHRPROASPVALGLUALALEU
14   ALAVALMETILEPROLYSGLULYSTYRPRO
15   ASNPROSERILEASPPHEASNGLYLEUVAL
16   PROALAGLYILEASNVALVALSERPROLYS
17   HISGLYTYRGLNLYSGLUGLUILEMETVAL
18   ILEASPGLULEUILEPHEASNILEASNTHR
19   LYSASPASPLEULYSLEUALAGLUMETLEU
20   LEULYSLYSASPGLYLEU

Samples:

sample_1: CobY, [U-100% 15N], 2.0 mM; H2O 95%; D2O 5%; TRIS 50 mM; DTT 5 mM; NaCl 50 mM; MgCl2 10 mM

sample_2: CobY, [U-100% 13C; U-100% 15N], 2.0 mM; H2O 95%; D2O 5%; TRIS 50 mM; DTT 5 mM; NaCl 50 mM; MgCl2 10 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7; pressure: 1 atm; temperature: 313 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCACBsample_2isotropicsample_conditions_1
3D CBCA(CO)NHsample_2isotropicsample_conditions_1
3D HNCOsample_2isotropicsample_conditions_1
3D H(CCO)NHsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_2isotropicsample_conditions_1

Software:

X-PLOR_NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement

VNMRJ, Varian - collection

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

XEASY, Bartels et al. - data analysis

TALOS, Cornilescu, Delaglio and Bax - data analysis

SPARKY, Goddard - data analysis

CYANA, Guntert, Mumenthaler and Wuthrich - chemical shift assignment, structure solution

Molmol, Koradi, Billeter and Wuthrich - data analysis

Procheck, Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thornton - structure solution

NMR spectrometers:

  • Varian INOVA 900 MHz
  • Varian INOVA 800 MHz
  • Varian INOVA 600 MHz

Related Database Links:

PDB
GB AAB99118
SP Q58517

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