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BMRB: 16011

8R5V

NMR Spectroscopic Characterization of 13C, 15N-labeled Ribonuclease A in urea 8M

Authors

Lopez-Alonso, J.P., Bruix, M., Font, J., Ribo, M., Vilanova, M., Morbio, M., Jimenez, M.A., Rico, M., Santoro, J., Gonzalez, C., Laurents, D.V.

Assembly

bovine pancreas ribonuclease A

Entity

1. bovine pancreas ribonuclease A (polymer, Thiol state: all disulfide bound), 124 monomers, 13690.17 Da Detail

KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHF DASV

Formula weight

13690.17 Da

Entity Connection

disulfide 4 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS26:SG	1:CYS84:SG
2	disulfide	sing	1:CYS40:SG	1:CYS95:SG
3	disulfide	sing	1:CYS58:SG	1:CYS110:SG
4	disulfide	sing	1:CYS65:SG	1:CYS72:SG

Source organism

Exptl. method

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.2 %, Completeness: 38.3 %, Completeness (bb): 66.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	38.3 % (527 of 1376)	22.0 % (157 of 714)	48.8 % (256 of 525)	83.2 % (114 of 137)
Backbone	66.2 % (487 of 736)	51.4 % (127 of 247)	66.9 % (247 of 369)	94.2 % (113 of 120)
Sidechain	20.5 % (156 of 761)	6.4 % (30 of 467)	45.1 % (125 of 277)	5.9 % (1 of 17)
Aromatic	0.0 % (0 of 94)	0.0 % (0 of 47)	0.0 % (0 of 47)
Methyl	25.0 % (25 of 100)	16.0 % (8 of 50)	34.0 % (17 of 50)

1. ribonuclease A

KETAAAKFER QHMDSSTSAA SSSNYCNQMM KSRNLTKDRC KPVNTFVHES LADVQAVCSQ KNVACKNGQT NCYQSYSTMS ITDCRETGSS KYPNCAYKTT QANKHIIVAC EGNPYVPVHF DASV

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

LACS Plot; CA

Referencing offset: -0.19 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.19 ppm, Outliers: 3 Detail

Release date

2010-10-17

Citation

NMR spectroscopy reveals that RNase A is chiefly denatured in 40% acetic acid: implications for oligomer formation by 3D domain swapping
Lopez-Alonso, J., Bruix, M., Font, J., Ribo, M., Vilanova, M., Jimenez, M., Santoro, J., Gonzalez, C., Laurents, D.V.
J. Am. Chem. Soc. (2010), 132, 1621-1630, PubMed 20085318 , DOI 10.1021/ja9081638 , Abstract

Related entities 1. bovine pancreas ribonuclease A, : 1 : 101 : 139 entities Detail

Interaction partners 1. bovine pancreas ribonuclease A, : 8 interactors Detail

More details for 8 interactors identified by 6 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

2 2D 1H-13C HSQC

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

3 2D 1H-1H NOESY

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

4 3D HNCA

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

5 3D HNCACB

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

6 3D CBCA(CO)NH

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

7 3D HN(CO)CA

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

8 2D CB-edited 1H-15N HSQC

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

9 2D CG-edited 1H-15N HSQC

Instrument

Bruker Avance US2 NMR - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±0.1) K, pH 2.0 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	ribonuclease A	[U-98% 13C; U-98% 15N]		1.75 mM
2	H2O	natural abundance		90 %
3	D2O	natural abundance		10 %
4	urea	natural abundance		8 M

Chemical shift validation 3 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr16011_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	OK

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:26:CYS:SG	1:84:CYS:SG	oxidized, CA 55.59, CB 40.3 ppm	oxidized, CA 55.26, CB 40.49 ppm	n/a
1:40:CYS:SG	1:95:CYS:SG	oxidized, CA 54.95, CB 40.86 ppm	unknown, CA 55.16 ppm	n/a
1:58:CYS:SG	1:110:CYS:SG	oxidized, CA 55.31, CB 40.84 ppm	oxidized, CA 55.22, CB 40.78 ppm	n/a
1:65:CYS:SG	1:72:CYS:SG	oxidized, CA 55.04, CB 40.8 ppm	oxidized, CA 56.5, CB 41.36 ppm	n/a

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Content subtype: bmr16011_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	463		99.2 (chain: 1, length: 124)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 124, Sequence coverage: 99.2%
- Total number of assignments
  - ¹³C chemical shifts: 239
  - ¹H chemical shifts: 112
  - ¹⁵N chemical shifts: 112
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1