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Found 1 Document (1.043 seconds)

BMRB: 25942

2NAM

Full-length WT SOD1 in DPC MICELLE

Authors

Lim, L., Song, J.

Assembly

Full-length WT SOD1

Entity

1. Full-length WT SOD1 (polymer), 161 monomers, 16815.44 Da Detail

MGHHHHHHAT KAVCVLKGDG PVQGIINFEQ KESNGPVKVW GSIKGLTEGL HGFHVHEFGD NTAGCTSAGP HFNPLSRKHG GPKDEERHVG DLGNVTADKD GVADVSIEDS VISLSGDHCI IGRTLVVHEK ADDLGKGGNE ESTKTGNAGS RLACGVIGIA Q

Formula weight

16815.44 Da

Source organism

Escherichia coli

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.7 %, Completeness: 62.9 %, Completeness (bb): 77.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	62.9 % (1078 of 1713)	70.5 % (620 of 880)	45.3 % (302 of 666)	93.4 % (156 of 167)
Backbone	77.7 % (743 of 956)	89.2 % (306 of 343)	63.7 % (291 of 457)	93.6 % (146 of 156)
Sidechain	51.9 % (463 of 892)	58.5 % (314 of 537)	40.4 % (139 of 344)	90.9 % (10 of 11)
Aromatic	3.7 % (4 of 108)	3.7 % (2 of 54)	3.8 % (2 of 53)	0.0 % (0 of 1)
Methyl	44.5 % (73 of 164)	73.2 % (60 of 82)	15.9 % (13 of 82)

1. entity

MGHHHHHHAT KAVCVLKGDG PVQGIINFEQ KESNGPVKVW GSIKGLTEGL HGFHVHEFGD NTAGCTSAGP HFNPLSRKHG GPKDEERHVG DLGNVTADKD GVADVSIEDS VISLSGDHCI IGRTLVVHEK ADDLGKGGNE ESTKTGNAGS RLACGVIGIA Q

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 313 K, pH 4

#	Name	Isotope labeling	Type	Concentration
1	DPC	natural abundance		20 mM
2	entity	[U-13C; U-15N]		0.4 mM

LACS Plot; CA

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

Referencing offset: -0.33 ppm, Outliers: 1 Detail

LACS Plot; CB

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

Referencing offset: -0.33 ppm, Outliers: 1 Detail

LACS Plot; HA

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

Referencing offset: 0.01 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 5 models in PDB: 2NAM, Strand ID: A Detail

Release date

2016-01-13

Citation

SALS-linked WT-SOD1 adopts a highly similar helical conformation as FALS-causing L126Z-SOD1 in a membrane environment
Lim, L., Song, J.
Biochim. Biophys. Acta (2016), 1858, 2223-2230, PubMed 27378311 , DOI 10.1016/j.bbamem.2016.06.027 , Abstract

Related entities 1. Full-length WT SOD1, : 1 : 93 : 156 entities Detail

Interaction partners 1. Full-length WT SOD1, : 26 interactors Detail

More details for 26 interactors identified by 11 citations

Experiments performed 5 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25942_2nam.nef
Input source #2: Coordindates	2nam.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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

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

-----100-------110-------120-------130-------140-------150---
GVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
-------110-------120-------130-------140-------150-------160-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	161	0	0	100.0

Content subtype: combined_25942_2nam.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1040		95.0 (chain: A, length: 161)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	698 (1)	noe	91.3 (chain: A, length: 161)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	155 (155)	.	63.4 (chain: A, length: 161)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 95.0%
- Total number of assignments
  - ¹H chemical shifts: 603
  - ¹³C chemical shifts: 279
  - ¹⁵N chemical shifts: 158
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
69	ARG	HH11	6.66
69	ARG	HH21	6.705
79	ARG	HH11	6.676
79	ARG	HH21	6.741
115	ARG	HH12	6.756
115	ARG	HH21	6.756
143	ARG	HH11	6.798
143	ARG	HH21	6.798

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	880	595	67.6
¹³C chemical shifts	666	279	41.9
¹⁵N chemical shifts	171	158	92.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	343	299	87.2
¹³C chemical shifts	322	152	47.2
¹⁵N chemical shifts	156	144	92.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	537	296	55.1
¹³C chemical shifts	344	127	36.9
¹⁵N chemical shifts	15	14	93.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	59	71.1
¹³C chemical shifts	83	10	12.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	0	0.0
¹³C chemical shifts	53	0	0.0
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 91.3%
- Total number of restraints: 698
- Weight of restraints: 1.0 (698)
- Potential type of restraints: upper-bound-parabolic (698)
- Range of distance target values: 3.04, 7.58 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 161, Sequence coverage: 63.4%
- Total number of restraints: 155
- Total number of restraints per polymer type: 155
- Weight of restraints: 1.0 (155)
- Potential type of restraints: square-well-parabolic (155)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DPC MICELLE, Full length SOD1, Superoxide Dismutase 1, phospholipid interaction

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Found 1 Document (1.043 seconds)

BMRB: 25942

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Full-length WT SOD1, : 1 : 93 : 156 entities Detail

Interaction partners 1. Full-length WT SOD1, : 26 interactors Detail

Experiments performed 5 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail