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Found 1 Document (1.059 seconds)

BMRB: 15845

2K5O

Mouse Prion Protein (121-231) with Mutation S170N

Authors

Perez, D.R., Wuthrich, K.

Assembly

Prion Protein

Entity

1. Prion Protein (polymer, Thiol state: all disulfide bound), 114 monomers, 13420.77 Da Detail

GSVVGGLGGY MLGSAMSRPM IHFGNDWEDR YYRENMYRYP NQVYYRPVDQ YNNQNNFVHD CVNITIKQHT VTTTTKGENF TETDVKMMER VVEQMCVTQY QKESQAYYDG RRSS

Formula weight

13420.77 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS61:SG	1:CYS96:SG

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

OPAL (water shell)

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 71.0 %, Completeness (bb): 70.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	71.0 % (952 of 1341)	62.9 % (440 of 700)	75.0 % (384 of 512)	99.2 % (128 of 129)
Backbone	70.9 % (481 of 678)	58.1 % (136 of 234)	70.6 % (235 of 333)	99.1 % (110 of 111)
Sidechain	75.0 % (576 of 768)	65.2 % (304 of 466)	89.4 % (254 of 284)	100.0 % (18 of 18)
Aromatic	43.7 % (62 of 142)	28.2 % (20 of 71)	58.6 % (41 of 70)	100.0 % (1 of 1)
Methyl	57.0 % (49 of 86)	14.0 % (6 of 43)	100.0 % (43 of 43)

1. Prion Protein

GSVVGGLGGY MLGSAMSRPM IHFGNDWEDR YYRENMYRYP NQVYYRPVDQ YNNQNNFVHD CVNITIKQHT VTTTTKGENF TETDVKMMER VVEQMCVTQY QKESQAYYDG RRSS

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.2 K, pH 4.5

#	Name	Isotope labeling	Concentration
1	Prion Protein	[U-99% 13C; U-99% 15N]	0.4 mM
2	D2O	natural abundance	10 %
3	H2O	natural abundance	90 %
4	sodium acetate	[U-2H]	10 mM
5	sodium azide	natural abundance	0.02 %

LACS Plot; CA

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

Referencing offset: 0.54 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: 0.54 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.14 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2K5O, Strand ID: A Detail

Release date

2008-09-11

Citation

NMR structure of the bank vole prion protein at 20 degrees C contains a structured loop of residues 165-171
Christen, B., Perez, D.R., Hornemann, S., Wuthrich, K.
J. Mol. Biol. (2008), 383, 306-312, PubMed 18773909 , DOI 10.1016/j.jmb.2008.08.045 , Abstract

Related entities 1. Prion Protein, : 1 : 9 : 1 : 146 entities Detail

Interaction partners 1. Prion Protein, : 36 interactors Detail

More details for 36 interactors identified by 12 citations

Experiments performed 2 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15845_2k5o.nef
Input source #2: Coordindates	2k5o.cif
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	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:179:CYS:SG	A:214:CYS:SG	oxidized, CA 58.119, CB 40.215 ppm	oxidized, CA 59.439, CB 41.386 ppm	2.048

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

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

-120-----130-------140-------150-------160-------170-------180-------190-------200-------210-------2
GSVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQY
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSVVGGLGGYMLGSAMSRPMIHFGNDWEDRYYRENMYRYPNQVYYRPVDQYNNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCVTQY
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

20-------230--
QKESQAYYDGRRSS
||||||||||||||
QKESQAYYDGRRSS
-------110----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	114	0	0	100.0

Content subtype: combined_15845_2k5o.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	898		99.1 (chain: A, length: 114)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	1722 (1)	noe	99.1 (chain: A, length: 114)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 396
  - ¹³C chemical shifts: 367
  - ¹⁵N chemical shifts: 135
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
156	ARG	HH21	6.343
183	THR	HG1	6.313

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	700	394	56.3
¹³C chemical shifts	512	367	71.7
¹⁵N chemical shifts	137	135	98.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	234	110	47.0
¹³C chemical shifts	228	113	49.6
¹⁵N chemical shifts	111	110	99.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	466	284	60.9
¹³C chemical shifts	284	254	89.4
¹⁵N chemical shifts	26	25	96.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	0	0.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	14	19.7
¹³C chemical shifts	70	41	58.6
¹⁵N chemical shifts	1	1	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 114, Sequence coverage: 99.1%
- Total number of restraints: 1721
- Weight of restraints: 1.0 (1721)
- Potential type of restraints: upper-bound-parabolic (1721)
- Range of distance target values: 2.47, 5.5 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords bank vole, mouse prion protein, mutation, S170N

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Found 1 Document (1.059 seconds)

BMRB: 15845

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Prion Protein, : 1 : 9 : 1 : 146 entities Detail

Interaction partners 1. Prion Protein, : 36 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail