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BMRB: 17595

2LCQ

NMR resonance assignments for an archaeal homolog of the endonuclease Nob1 involved in ribosome biogenesis

Authors

Veith, T., Wurm, J.P., Duchardt-Ferner, E., Weis, B., Hennig, R., Martin, R., Safferthal, C., Bohnsack, M.T., Schleiff, E., Woehnert, J.

Assembly

Nob1

Entity

1. PhNob1 (polymer, Thiol state: all other bound), 161 monomers, 17971.87 Da Detail

MLRNLKKTLV LDSSVFIQGI DIEGYTTPSV VEEIKDRESK IFLESLISAG KVKIAEPSKE SIDRIIQVAK ETGEVNELSK ADIEVLALAY ELKGEIFSDD YNVQNIASLL GLRFRTLKRG IKKVIKWRYV CIGCGRKFST LPPGGVCPDC GSKVKLIPRK R

2. ZN (non-polymer), 65.409 Da

Total weight

18037.277 Da

Max. entity weight

17971.87 Da

Entity Connection

na 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:CYS131:SG	2:ZN1:ZN
2	na	sing	1:CYS134:SG	2:ZN1:ZN
3	na	sing	1:CYS147:SG	2:ZN1:ZN
4	na	sing	1:CYS150:SG	2:ZN1:ZN

Source organism

Pyrococcus horikoshii

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.8 %, Completeness: 93.0 %, Completeness (bb): 98.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.0 % (1789 of 1924)	91.1 % (919 of 1009)	94.4 % (710 of 752)	98.2 % (160 of 163)
Backbone	98.2 % (937 of 954)	97.9 % (321 of 328)	98.5 % (464 of 471)	98.1 % (152 of 155)
Sidechain	89.3 % (999 of 1119)	87.8 % (598 of 681)	91.4 % (393 of 430)	100.0 % (8 of 8)
Aromatic	80.9 % (76 of 94)	100.0 % (47 of 47)	60.9 % (28 of 46)	100.0 % (1 of 1)
Methyl	94.8 % (199 of 210)	93.3 % (98 of 105)	96.2 % (101 of 105)

1. PhNob1

MLRNLKKTLV LDSSVFIQGI DIEGYTTPSV VEEIKDRESK IFLESLISAG KVKIAEPSKE SIDRIIQVAK ETGEVNELSK ADIEVLALAY ELKGEIFSDD YNVQNIASLL GLRFRTLKRG IKKVIKWRYV CIGCGRKFST LPPGGVCPDC GSKVKLIPRK R

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Concentration
1	PhNob1	[U-15N]	0.4 mM
2	potassium chloride	natural abundance	50 mM
3	BisTris	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 310 K, pH 6.2

#	Name	Isotope labeling	Concentration
6	PhNob1	[U-13C; U-15N]	0.4 mM
7	potassium chloride	natural abundance	50 mM
8	BisTris	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D20	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: -0.12 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.12 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.0 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.21 ppm, Outliers: 4 Detail

Protein Blocks Logo

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

Release date

2011-04-18

Citation

Structural and functional analysis of the archaeal endonuclease Nob1
Veith, T., Martin, R., Wurm, J.P., Weis, B.L., Duchardt-Ferner, E., Safferthal, C., Hennig, R., Mirus, O., Bohnsack, M.T., Wohnert, J., Schleiff, E.
Nucleic Acids Res. (2012), 40, 3259-3274, PubMed 22156373 , DOI 10.1093/nar/gkr1186 , Abstract

Related entities 1. PhNob1, : 1 : 1 : 6 entities Detail

Experiments performed 19 experiments Detail

1 3D HNCACB