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Found 1 Document (1.366 seconds)

BMRB: 15142

2E8J

Solution structure of dynein light chain 2A

Authors

Kouno, T., Nabeshima, Y., Mizuguchi, M., Kawano, K.

Assembly

DL2A homodimer

Entity

1. DL2A homodimer (polymer, Thiol state: not present), 101 monomers, 11332.92 × 2 Da Detail

GPLGSMAEVE ETLKRLQSQK GVQGIIVVNT EGIPIKSTMD NPTTTQYASL MHSFILKARS TVRDIDPQND LTFLRIRSKK NEIMVAPDKD YFLIVIQNPT E

Total weight

22665.84 Da

Max. entity weight

11332.92 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

distance geometry, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.1 %, Completeness: 78.0 %, Completeness (bb): 78.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	78.0 % (930 of 1193)	84.3 % (526 of 624)	67.8 % (314 of 463)	84.9 % (90 of 106)
Backbone	78.8 % (468 of 594)	91.5 % (184 of 201)	65.1 % (194 of 298)	94.7 % (90 of 95)
Sidechain	79.7 % (554 of 695)	80.9 % (342 of 423)	81.2 % (212 of 261)	0.0 % (0 of 11)
Aromatic	4.0 % (2 of 50)	8.0 % (2 of 25)	0.0 % (0 of 25)
Methyl	92.1 % (116 of 126)	92.1 % (58 of 63)	92.1 % (58 of 63)

1. Dynein light chain 2A, cytoplasmic

GPLGSMAEVE ETLKRLQSQK GVQGIIVVNT EGIPIKSTMD NPTTTQYASL MHSFILKARS TVRDIDPQND LTFLRIRSKK NEIMVAPDKD YFLIVIQNPT E

Show sample condition

Sample #1

Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
1	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	0.1 mM
4	EDTA	natural abundance	20 mM
5	H2O		95 %
6	D2O		5 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 100% D2O

#	Name	Isotope labeling	Concentration
7	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
8	phosphate buffer	natural abundance	20 mM
9	NaCl	natural abundance	0.1 mM
10	EDTA	natural abundance	20 mM
11	D2O		100 %

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: -0.11 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: -0.11 ppm, Outliers: 1 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	direct	1.0
¹⁵N	DSS	methyl protons	internal	indirect	0.1013291

Referencing offset: -0.14 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 1 models in PDB: 2E8J, Strand ID: A, B Detail

Release date

2009-10-14

Citation

Solution structure of dynein light chain 2A
Kouno, T., Nabeshima, Y., Mizuguchi, M., Kawano, K.

Related entities 1. DL2A homodimer, : 1 : 21 : 59 entities Detail

Interaction partners 1. DL2A homodimer, : 32 interactors Detail

More details for 32 interactors identified by 12 citations

Experiments performed 7 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 95% H2O, 5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 95% H2O, 5% D2O

#	Name	Isotope labeling	Concentration
1	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	0.1 mM
4	EDTA	natural abundance	20 mM
5	H2O		95 %
6	D2O		5 %

2 3D_13C-separated_NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 100% D2O

#	Name	Isotope labeling	Concentration
7	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
8	phosphate buffer	natural abundance	20 mM
9	NaCl	natural abundance	0.1 mM
10	EDTA	natural abundance	20 mM
11	D2O		100 %

3 2D NOESY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 100% D2O

#	Name	Isotope labeling	Concentration
7	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
8	phosphate buffer	natural abundance	20 mM
9	NaCl	natural abundance	0.1 mM
10	EDTA	natural abundance	20 mM
11	D2O		100 %

4 3D CBCA(CO)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	0.1 mM
4	EDTA	natural abundance	20 mM
5	H2O		95 %
6	D2O		5 %

5 3D HBHA(CO)NH

Instrument

Bruker AVANCE - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
2	phosphate buffer	natural abundance	20 mM
3	NaCl	natural abundance	0.1 mM
4	EDTA	natural abundance	20 mM
5	H2O		95 %
6	D2O		5 %

6 3D HCCH-COSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 100% D2O

#	Name	Isotope labeling	Concentration
7	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
8	phosphate buffer	natural abundance	20 mM
9	NaCl	natural abundance	0.1 mM
10	EDTA	natural abundance	20 mM
11	D2O		100 %

7 3D HCCH-TOCSY

Instrument

Bruker AVANCE - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 0.6mM DL2A U-15, 13C; 20mM phosphate buffer NA; 20mM NaCl; 0.1mM EDTA; 100% D2O

#	Name	Isotope labeling	Concentration
7	Dynein light chain 2A, cytoplasmic	[U-100% 13C; U-100% 15N]	0.6 mM
8	phosphate buffer	natural abundance	20 mM
9	NaCl	natural abundance	0.1 mM
10	EDTA	natural abundance	20 mM
11	D2O		100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_15142_2e8j.nef
Input source #2: Coordindates	2e8j.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-----
GPLGSMAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPLGSMAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDIDPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPT
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-
E
|
E
-

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

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

-
E
|
E
-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	101	0	0	100.0
B	B	101	0	0	100.0

Content subtype: combined_15142_2e8j.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	928		94.1 (chain: A, length: 101)
1	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	3070 (1)	noe	94.1 (chain: A, length: 101), 94.1 (chain: B, length: 101)
2	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	72 (1)	hbond	22.8 (chain: A, length: 101), 22.8 (chain: B, length: 101)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 533
  - ¹³C chemical shifts: 305
  - ¹⁵N chemical shifts: 90
- 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 (%)
¹H chemical shifts	624	533	85.4
¹³C chemical shifts	463	305	65.9
¹⁵N chemical shifts	111	90	81.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	201	188	93.5
¹³C chemical shifts	202	95	47.0
¹⁵N chemical shifts	95	90	94.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	423	345	81.6
¹³C chemical shifts	261	210	80.5
¹⁵N chemical shifts	16	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	58	86.6
¹³C chemical shifts	67	57	85.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	25	0	0.0
¹³C chemical shifts	25	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 94.1%
  - Entity_assembly_ID: B, Chain length: 101, Sequence coverage: 94.1%
- Total number of restraints: 3063
- Weight of restraints: 1.0 (3063)
- Potential type of restraints: square-well-parabolic (3063)
- Range of distance target values: 2.3, 4.4 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_2
  - Status: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 101, Sequence coverage: 22.8%
    - Entity_assembly_ID: B, Chain length: 101, Sequence coverage: 22.8%
  - Total number of restraints: 72
  - Weight of restraints: 1.0 (72)
  - Potential type of restraints: square-well-parabolic (72)
  - Range of distance target values: 1.8, 2.8 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
  - Distance restraints on contact map

Keywords homodimer

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Found 1 Document (1.366 seconds)

BMRB: 15142

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DL2A homodimer, : 1 : 21 : 59 entities Detail

Interaction partners 1. DL2A homodimer, : 32 interactors Detail

Experiments performed 7 experiments Detail

Instrument

Sample

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Sample

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Sample

NMR combined restraints 4 contents Detail