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BMRB: 15394

2JOH

NMR structure of rabbit prion protein mutation S173N

Authors

Li, J., Lin, D.

Assembly

rpp mutation S173N

Entity

1. rpp mutation S173N (polymer, Thiol state: all disulfide bound), 138 monomers, 15705.36 Da Detail

QGGTHNQWGK PSKPKTSMKH VAPAAAAGAV VGGLGGYMLG SAMSRPLIHF GNDYEDRYYR ENMYRYPNQV YYRPVDQYSN QNNFVHDCVN ITVKQHTVTT TTKGENFTET DIKIMERVVE QMCITQYQQE SQAAYQRA

Formula weight

15705.36 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS88:SG	1:CYS123:SG

Source organism

Oryctolagus cuniculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.1 %, Completeness: 69.7 %, Completeness (bb): 77.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.7 % (1115 of 1600)	74.5 % (621 of 834)	59.6 % (365 of 612)	83.8 % (129 of 154)
Backbone	77.2 % (630 of 816)	88.3 % (248 of 281)	63.3 % (255 of 403)	96.2 % (127 of 132)
Sidechain	64.9 % (591 of 911)	67.5 % (373 of 553)	64.3 % (216 of 336)	9.1 % (2 of 22)
Aromatic	27.3 % (41 of 150)	49.3 % (37 of 75)	5.4 % (4 of 74)	0.0 % (0 of 1)
Methyl	84.7 % (100 of 118)	81.4 % (48 of 59)	88.1 % (52 of 59)

1. rpp mutation S173N

QGGTHNQWGK PSKPKTSMKH VAPAAAAGAV VGGLGGYMLG SAMSRPLIHF GNDYEDRYYR ENMYRYPNQV YYRPVDQYSN QNNFVHDCVN ITVKQHTVTT TTKGENFTET DIKIMERVVE QMCITQYQQE SQAAYQRA

Show sample condition

Sample #1

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.13 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	rpp S173N	[U-13C; U-15N]		0.8 ~ 1.0 mM
2	sodium acetate	natural abundance		20 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298.13 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
3	rpp S173N	[U-15N]		0.8 ~ 1.0 mM
4	sodium acetate	natural abundance		20 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	internal	indirect	1.0
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	nitrogen	internal	indirect	1.0

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	internal	indirect	1.0
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	nitrogen	internal	indirect	1.0

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbon	internal	indirect	1.0
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	nitrogen	internal	indirect	1.0

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 15 models in PDB: 2JOH, Strand ID: A Detail

Release date

2010-11-14

Citation

Unique structural characteristics of the rabbit prion protein
Wen, Y., Li, J., Yao, W., Xiong, M., Hong, J., Peng, Y., Xiao, G., Lin, D.
J. Biol. Chem. (2010), 285, 31682-31693, PubMed 20639199 , DOI 10.1074/jbc.M110.118844 , Abstract

Related entities 1. rpp mutation S173N, : 1 : 114 entities Detail

Interaction partners 1. rpp mutation S173N, : 1 interactors Detail

More details for 1 interactors identified by 1 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_15394_2joh.nef
Input source #2: Coordindates	2joh.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:178:CYS:SG	A:213:CYS:SG	oxidized, CA 58.693, CB 41.067 ppm	oxidized, CA 60.057, CB 42.1 ppm	2.021

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

-90------100-------110-------120-------130-------140-------150-------160-------170-------180-------1
MHQGGTHNQWGKPSKPKTSMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHQGGTHNQWGKPSKPKTSMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNNFVHDCVNITVKQHTV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

90-------200-------210-------220-------230------
TTTTKGENFTETDIKIMERVVEQMCITQYQQESQAAYQRALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||
TTTTKGENFTETDIKIMERVVEQMCITQYQQESQAAYQRALEHHHHHH
-------110-------120-------130-------140--------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	148	0	0	100.0

Content subtype: combined_15394_2joh.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	1049		89.9 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2847 (1)	noe	70.9 (chain: A, length: 148)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 89.9%
- Total number of assignments
  - ¹H chemical shifts: 607
  - ¹⁵N chemical shifts: 125
  - ¹³C chemical shifts: 317
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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)
139	HIS	HD1	12.632
139	HIS	HE2	6.573

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	892	605	67.8
¹⁵N chemical shifts	172	125	72.7
¹³C chemical shifts	659	317	48.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	303	247	81.5
¹⁵N chemical shifts	143	125	87.4
¹³C chemical shifts	296	114	38.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	589	358	60.8
¹⁵N chemical shifts	29	0	0.0
¹³C chemical shifts	363	203	55.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	54	79.4
¹³C chemical shifts	68	55	80.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	35	39.3
¹⁵N chemical shifts	1	0	0.0
¹³C chemical shifts	88	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 148, Sequence coverage: 70.9%
- Total number of restraints: 2846
- Weight of restraints: 1.0 (2846)
- Potential type of restraints: square-well-parabolic (2846)
- Range of distance target values: 1.75, 4.0 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Keywords prion protein

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Found 1 Document (0.702 seconds)

BMRB: 15394

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. rpp mutation S173N, : 1 : 114 entities Detail

Interaction partners 1. rpp mutation S173N, : 1 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail