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Found 1 Document (0.769 seconds)

BMRB: 15399

2JOM

NMR structure of rabbit prion protein mutation I214V

Authors

Li, J., Lin, D.

Assembly

rpp I214V

Entity

1. rpp I214V (polymer, Thiol state: all disulfide bound), 138 monomers, 15624.24 Da Detail

QGGTHNQWGK PSKPKTSMKH VAGAAAAGAV VGGLGGYMLG SAMSRPLIHF GNDYEDRYYR ENMYRYPNQV YYRPVDQYSN QNSFVHDCVN ITVKQHTVTT TTKGENFTET DIKIMERVVE QMCVTQYQQE SQAAYQRA

Formula weight

15624.24 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: 100.0 %, Completeness: 92.1 %, Completeness (bb): 97.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.1 % (1463 of 1588)	94.7 % (782 of 826)	87.3 % (531 of 608)	97.4 % (150 of 154)
Backbone	97.9 % (801 of 818)	97.9 % (277 of 283)	97.5 % (392 of 402)	99.2 % (132 of 133)
Sidechain	87.7 % (786 of 896)	93.0 % (505 of 543)	79.2 % (263 of 332)	85.7 % (18 of 21)
Aromatic	46.0 % (69 of 150)	78.7 % (59 of 75)	12.2 % (9 of 74)	100.0 % (1 of 1)
Methyl	99.2 % (117 of 118)	98.3 % (58 of 59)	100.0 % (59 of 59)

1. rpp I214V

QGGTHNQWGK PSKPKTSMKH VAGAAAAGAV VGGLGGYMLG SAMSRPLIHF GNDYEDRYYR ENMYRYPNQV YYRPVDQYSN QNSFVHDCVN ITVKQHTVTT TTKGENFTET DIKIMERVVE QMCVTQYQQE SQAAYQRA

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298.13 K, pH 4.5

#	Name	Isotope labeling	Type	Concentration
1	rpp I214V	[U-13C; U-15N]		0.7 ~ 0.8 mM
2	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 protons	internal	indirect	0.2514495
¹H	DSS	methyl protons	internal	indirect	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.2 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: 0.05 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: -0.16 ppm, Outliers: 3 Detail

Protein Blocks Logo

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

Release date

2010-10-18

Citation

Solution structure and dynamics of the I214V mutant of the rabbit prion protein
Wen, Y., Li, J., Xiong, M., Peng, Y., Yao, W., Hong, J., Lin, D.
PLoS One (2010), 5, e13273-e13273, PubMed 20949107 , DOI 10.1371/journal.pone.0013273 , Abstract

Related entities 1. rpp I214V, : 1 : 3 : 111 entities Detail

Interaction partners 1. rpp I214V, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 1 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15399_2jom.nef
Input source #2: Coordindates	2jom.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 58.992, CB 41.445 ppm	oxidized, CA 60.243, CB 42.406 ppm	2.032

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
MHQGGTHNQWGKPSKPKTSMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHQGGTHNQWGKPSKPKTSMKHVAGAAAAGAVVGGLGGYMLGSAMSRPLIHFGNDYEDRYYRENMYRYPNQVYYRPVDQYSNQNSFVHDCVNITVKQHTV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

90-------200-------210-------220-------230------
TTTTKGENFTETDIKIMERVVEQMCVTQYQQESQAAYQRALEHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||
TTTTKGENFTETDIKIMERVVEQMCVTQYQQESQAAYQRALEHHHHHH
-------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_15399_2jom.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	1486		93.2 (chain: A, length: 148)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2655 (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: 93.2%
- Total number of assignments
  - ¹H chemical shifts: 798
  - ¹³C chemical shifts: 532
  - ¹⁵N chemical shifts: 156
- 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)
110	HIS	HD1	7.096
127	TYR	HH	8.591
139	HIS	HD1	12.479
139	HIS	HE2	6.577
149	TYR	HH	6.936
161	TYR	HH	8.59
176	HIS	HD1	7.352
176	HIS	HE2	8.118

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	888	790	89.0
¹³C chemical shifts	658	532	80.9
¹⁵N chemical shifts	171	156	91.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	303	281	92.7
¹³C chemical shifts	296	271	91.6
¹⁵N chemical shifts	143	132	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	585	509	87.0
¹³C chemical shifts	362	261	72.1
¹⁵N chemical shifts	28	24	85.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	68	64	94.1
¹³C chemical shifts	68	65	95.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	55	61.8
¹³C chemical shifts	88	4	4.5
¹⁵N chemical shifts	1	1	100.0

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: 2651
- Weight of restraints: 1.0 (2651)
- Potential type of restraints: square-well-parabolic (2651)
- Range of distance target values: 1.65, 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 (0.769 seconds)

BMRB: 15399

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. rpp I214V, : 1 : 3 : 111 entities Detail

Interaction partners 1. rpp I214V, : 1 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 3 contents Detail