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BMRB: 25482

2MZB

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

Authors

Singarapu, K., Otte, M., Tonelli, M., Westler, W.M., Escalante-Semerena, J.C., Markley, J.L.

Assembly

GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY)

Entity

1. GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY) (polymer, Thiol state: all free), 196 monomers, 21745.25 Da Detail

MDALIMAGGK GTRMGGVEKP LIKLCGRCLI DYVVSPLLKS KVNNIFIATS PNTPKTKEYI NSAYKDYKNI VVIDTSGKGY IEDLNECIGY FSEPFLVVSS DLINLKSKII NSIVDYFYCI KAKTPDVEAL AVMIPKEKYP NPSIDFNGLV PAGINVVSPK HGYQKEEIMV IDELIFNINT KDDLKLAEML LKKDGL

Formula weight

21745.25 Da

Source organism

Methanocaldococcus jannaschii

Exptl. method

solution NMR

Refine. method

DGSA-distance geometry simulated annealing, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 85.3 %, Completeness (bb): 88.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	85.3 % (1989 of 2333)	91.8 % (1114 of 1214)	77.7 % (715 of 920)	80.4 % (160 of 199)
Backbone	88.3 % (1019 of 1154)	92.4 % (364 of 394)	87.3 % (502 of 575)	82.7 % (153 of 185)
Sidechain	83.6 % (1138 of 1362)	91.5 % (750 of 820)	72.2 % (381 of 528)	50.0 % (7 of 14)
Aromatic	35.4 % (51 of 144)	70.8 % (51 of 72)	0.0 % (0 of 72)
Methyl	95.2 % (240 of 252)	94.4 % (119 of 126)	96.0 % (121 of 126)

1. CobY

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7

#	Name	Isotope labeling	Concentration
1	CobY	[U-100% 15N]	2.0 mM
2	H2O	natural abundance	95 %
3	D2O	natural abundance	5 %
4	TRIS	natural abundance	50 mM
5	DTT	natural abundance	5 mM
6	NaCl	natural abundance	50 mM
7	MgCl2	natural abundance	10 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 313 K, pH 7

#	Name	Isotope labeling	Concentration
8	CobY	[U-100% 13C; U-100% 15N]	2.0 mM
9	H2O	natural abundance	95 %
10	D2O	natural abundance	5 %
11	TRIS	natural abundance	50 mM
12	DTT	natural abundance	5 mM
13	NaCl	natural abundance	50 mM
14	MgCl2	natural abundance	10 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.25 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.25 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.45 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MZB, Strand ID: A Detail

Release date

2015-11-08

Citation

Solution Structural Studies of GTP:Adenosylcobinamide-Phosphateguanylyl Transferase (CobY) from Methanocaldococcus jannaschii
Singarapu, K., Otte, M., Tonelli, M., Westler, W.M., Escalante-Semerena, J.C., Markley, J.L.
PLoS One (2015), 10, e0141297-e0141297, PubMed 26513744 , DOI 10.1371/journal.pone.0141297 , Abstract

Related entities 1. GTP:adenosylcobinamide-phosphate guanylyltransferase (CobY), : 1 : 2 : 1 : 9 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC