BMRBj - BMREntryMaster

Found 1 Document (0.754 seconds)

BMRB: 18880

2M1U

SOLUTION STRUCTURE OF THE SMALL DICTYOSTELIUM DISCOIDEIUM MYOSIN LIGHT CHAIN MlcB PROVIDES INSIGHTS INTO IQ-MOTIF RECOGNITION OF CLASS I MYOSIN MYO1B

Authors

Liburd, J., Chitayat, S., Crawley, S.W., Denis, C.M., Cote, G.P., Smith, S.P.

Assembly

MlcB

Entity

1. MlcB (polymer, Thiol state: not present), 93 monomers, 10459.28 Da Detail

MGSSHHHHHH SSGLVPRGSH MSDEKTQLIE AFYNFDGDYD GFVSVEEFRG IIRDGLPMTE AEITEFFEAA DPNNTGFIDY KAFAAMLYSV DES

Formula weight

10459.28 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 90.3 %, Completeness: 82.5 %, Completeness (bb): 87.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	82.5 % (861 of 1044)	83.3 % (445 of 534)	79.6 % (331 of 416)	90.4 % (85 of 94)
Backbone	87.9 % (485 of 552)	88.0 % (168 of 191)	87.1 % (236 of 271)	90.0 % (81 of 90)
Sidechain	78.5 % (453 of 577)	80.8 % (277 of 343)	74.8 % (172 of 230)	100.0 % (4 of 4)
Aromatic	36.4 % (51 of 140)	41.4 % (29 of 70)	31.4 % (22 of 70)
Methyl	100.0 % (74 of 74)	100.0 % (37 of 37)	100.0 % (37 of 37)

1. MlcB

MGSSHHHHHH SSGLVPRGSH MSDEKTQLIE AFYNFDGDYD GFVSVEEFRG IIRDGLPMTE AEITEFFEAA DPNNTGFIDY KAFAAMLYSV DES

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	MlcB	[U-100% 13C; U-100% 15N]	1 mM
8	HEPES	natural abundance	10 mM
9	sodium chloride	natural abundance	50 mM
10	DSS	natural abundance	0.5 mM
11	D2O	natural abundance	10 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	external	direct	1.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	nitrogen	external	direct	1.0

Referencing offset: -0.17 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	external	direct	1.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	nitrogen	external	direct	1.0

Referencing offset: -0.17 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	external	direct	1.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	nitrogen	external	direct	1.0

Referencing offset: 0.07 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl carbons	external	direct	1.0
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	nitrogen	external	direct	1.0

Referencing offset: -0.1 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 21 models in PDB: 2M1U, Strand ID: A Detail

Release date

2013-12-08

Citation

Structure of the small Dictyostelium discoideum myosin light chain MlcB provides insights into MyoB IQ motif recognition
Liburd, J., Chitayat, S., Crawley, S.W., Munro, K., Miller, E., Denis, C.M., Spencer, H.L., Cote, G.P., Smith, S.P.
J. Biol. Chem. (2014), 289, 17030-17042, PubMed 24790102 , DOI 10.1074/jbc.M113.536532 , Abstract

Related entities 1. MlcB, : 1 : 155 entities Detail

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 3D C(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

7 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	MlcB	[U-100% 13C; U-100% 15N]	1 mM
8	HEPES	natural abundance	10 mM
9	sodium chloride	natural abundance	50 mM
10	DSS	natural abundance	0.5 mM
11	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 3D H(CCO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
1	MlcB	[U-100% 13C; U-100% 15N]	1 mM
2	HEPES	natural abundance	10 mM
3	sodium chloride	natural abundance	50 mM
4	DSS	natural abundance	0.5 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	MlcB	[U-100% 13C; U-100% 15N]	1 mM
8	HEPES	natural abundance	10 mM
9	sodium chloride	natural abundance	50 mM
10	DSS	natural abundance	0.5 mM
11	D2O	natural abundance	10 %

13 2D 1H-1H NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	MlcB	[U-100% 13C; U-100% 15N]	1 mM
8	HEPES	natural abundance	10 mM
9	sodium chloride	natural abundance	50 mM
10	DSS	natural abundance	0.5 mM
11	D2O	natural abundance	10 %

14 2D 1H-1H TOCSY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Concentration
7	MlcB	[U-100% 13C; U-100% 15N]	1 mM
8	HEPES	natural abundance	10 mM
9	sodium chloride	natural abundance	50 mM
10	DSS	natural abundance	0.5 mM
11	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18880_2m1u.nef
Input source #2: Coordindates	2m1u.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---
MGSSHHHHHHSSGLVPRGSHMSDEKTQLIEAFYNFDGDYDGFVSVEEFRGIIRDGLPMTEAEITEFFEAADPNNTGFIDYKAFAAMLYSVDES
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGLVPRGSHMSDEKTQLIEAFYNFDGDYDGFVSVEEFRGIIRDGLPMTEAEITEFFEAADPNNTGFIDYKAFAAMLYSVDES

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	93	0	0	100.0

Content subtype: combined_18880_2m1u.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	848		90.3 (chain: A, length: 93)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1569 (1)	noe	77.4 (chain: A, length: 93)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	500 (1)	noe	53.8 (chain: A, length: 93)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	103 (103)	.	65.6 (chain: A, length: 93)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 90.3%
- Total number of assignments
  - ¹³C chemical shifts: 322
  - ¹H chemical shifts: 441
  - ¹⁵N chemical shifts: 85
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	416	322	77.4
¹H chemical shifts	534	441	82.6
¹⁵N chemical shifts	97	85	87.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	186	158	84.9
¹H chemical shifts	191	170	89.0
¹⁵N chemical shifts	90	80	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	230	164	71.3
¹H chemical shifts	343	271	79.0
¹⁵N chemical shifts	7	5	71.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	41	39	95.1
¹H chemical shifts	41	39	95.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	70	16	22.9
¹H chemical shifts	70	22	31.4

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 77.4%
- Total number of restraints: 1461
- Weight of restraints: 1.0 (1461)
- Potential type of restraints: square-well-parabolic (1461)
- Range of distance target values: 2.4, 3.9 (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_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 53.8%
  - Total number of restraints: 463
  - Weight of restraints: 1.0 (463)
  - Potential type of restraints: square-well-parabolic (463)
  - Range of distance target values: 2.4, 3.9 (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: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 93, Sequence coverage: 65.6%
- Total number of restraints: 103
- Total number of restraints per polymer type: 103
- Weight of restraints: 1.0 (103)
- Potential type of restraints: square-well-parabolic (103)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Mysoin light chain

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.754 seconds)

BMRB: 18880

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MlcB, : 1 : 155 entities Detail

Experiments performed 14 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail