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Found 1 Document (0.713 seconds)

BMRB: 30200

5TTT

Sparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta

Authors

Everett, J.K., Liu, G., Mao, B., Driscoll, M.A., Montelione, G.T.

Assembly

Degenerin mec-4

Entity

1. Degenerin mec-4 (polymer), 111 monomers, 13278.64 Da Detail

MSWMQNLKNY QHLRDPSEYM SQVYGDPLAY LQETTKFVTE REYYEDFGYG ECFNSTESEV QCELITGEFD PKLLPYDKRL AWHFKEFCYK TSAHGIPMIG EAPLEHHHHH H

Formula weight

13278.64 Da

Source organism

Caenorhabditis elegans

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.8 %, Completeness: 41.6 %, Completeness (bb): 74.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	41.6 % (561 of 1348)	22.1 % (155 of 702)	58.6 % (311 of 531)	82.6 % (95 of 115)
Backbone	74.8 % (489 of 654)	47.3 % (105 of 222)	88.7 % (290 of 327)	89.5 % (94 of 105)
Sidechain	20.9 % (167 of 799)	10.6 % (51 of 480)	37.2 % (115 of 309)	10.0 % (1 of 10)
Aromatic	6.3 % (12 of 192)	6.3 % (6 of 96)	5.3 % (5 of 94)	50.0 % (1 of 2)
Methyl	20.0 % (16 of 80)	15.0 % (6 of 40)	25.0 % (10 of 40)

1. entity 1

MSWMQNLKNY QHLRDPSEYM SQVYGDPLAY LQETTKFVTE REYYEDFGYG ECFNSTESEV QCELITGEFD PKLLPYDKRL AWHFKEFCYK TSAHGIPMIG EAPLEHHHHH H

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.8, Details 1.5 mM [U-13C; U-15N; U-2H] micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 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	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.52 ppm, Outliers: 1 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	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.52 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	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: 0.34 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5TTT, Strand ID: A Detail

Release date

2017-01-23

Citation

Sparse-restraint solution NMR structure of micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4 refined by restrained Rosetta
Everett, J.K., Liu, G., Mao, B., Driscoll, M.A., Montelione, G.T.

Related entities 1. Degenerin mec-4, : 1 : 1 : 2 : 1 entities Detail

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 300 K, pH 6.8, Details 1.5 mM [U-13C; U-15N; U-2H] micelle-solubilized cytosolic amino terminal domain of C. elegans mechanosensory ion channel MEC-4, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

2 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

4 3D HNCACO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

5 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

6 2D 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Type	Concentration
1	Degenerin mec-4	[U-13C; U-15N; U-2H]		1.5 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30200_5ttt.nef
Input source #2: Coordindates	5ttt.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-------100
MSWMQNLKNYQHLRDPSEYMSQVYGDPLAYLQETTKFVTEREYYEDFGYGECFNSTESEVQCELITGEFDPKLLPYDKRLAWHFKEFCYKTSAHGIPMIG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSWMQNLKNYQHLRDPSEYMSQVYGDPLAYLQETTKFVTEREYYEDFGYGECFNSTESEVQCELITGEFDPKLLPYDKRLAWHFKEFCYKTSAHGIPMIG

-------110-
EAPLEHHHHHH
|||||||||||
EAPLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	111	0	0	100.0

Content subtype: combined_30200_5ttt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	469		91.0 (chain: A, length: 111)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	6 (1)	noe	2.7 (chain: A, length: 111)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	Warning	154 (1)	noe	61.3 (chain: A, length: 111)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	50 (1)	hbond	38.7 (chain: A, length: 111)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	47 (47)	.	31.5 (chain: A, length: 111)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 91.0%
- Total number of assignments
  - ¹³C chemical shifts: 287
  - ¹H chemical shifts: 91
  - ¹⁵N chemical shifts: 91
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	531	287	54.0
¹H chemical shifts	702	91	13.0
¹⁵N chemical shifts	118	91	77.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	222	194	87.4
¹H chemical shifts	222	91	41.0
¹⁵N chemical shifts	105	91	86.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	309	93	30.1
¹H chemical shifts	480	0	0.0
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	44	4	9.1
¹H chemical shifts	44	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	94	0	0.0
¹H chemical shifts	96	0	0.0
¹⁵N chemical shifts	2	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 2.7%
- Total number of restraints: 6
- Weight of restraints: 1.0 (6)
- Potential type of restraints: square-well-parabolic (6)
- Range of distance target values: 4.2, 4.2 (Å)
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 61.3%
  - Total number of restraints: 154
  - Weight of restraints: 1.0 (154)
  - Potential type of restraints: square-well-parabolic (154)
  - Range of distance target values: 3.65, 6.95 (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
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 38.7%
    - Total number of restraints: 50
    - Weight of restraints: 1.0 (50)
    - Potential type of restraints: square-well-parabolic (50)
    - Range of distance target values: 2.0, 2.55 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 111, Sequence coverage: 31.5%
- Total number of restraints: 47
- Total number of restraints per polymer type: 47
- Weight of restraints: 1.0 (47)
- Potential type of restraints: square-well-parabolic (47)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords NESG, Northeast Structural Genomics Consortium, PSI-Biology, Structural Genomics, TRANSPORT PROTEIN

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Found 1 Document (0.713 seconds)

BMRB: 30200

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. Degenerin mec-4, : 1 : 1 : 2 : 1 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail