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BMRB: 18832

2M0Y

Solution structure of the SH3 domain of DOCK180

Authors

Liu, X., Wen, W.

Assembly

SH3 domain of DOCK180

Entity

1. SH3 domain of DOCK180 (polymer, Thiol state: not present), 74 monomers, 8645.725 Da Detail

MTRWVPTKRE EKYGVAFYNY DARGADELSL QIGDTVHILE TYEGWYRGYT LRKKSKKGIF PASYIHLKEA IVEG

Formula weight

8645.725 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.6 %, Completeness: 77.6 %, Completeness (bb): 75.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	77.6 % (698 of 899)	89.5 % (419 of 468)	61.4 % (218 of 355)	80.3 % (61 of 76)
Backbone	75.7 % (333 of 440)	90.2 % (138 of 153)	63.3 % (136 of 215)	81.9 % (59 of 72)
Sidechain	81.2 % (427 of 526)	89.2 % (281 of 315)	69.6 % (144 of 207)	50.0 % (2 of 4)
Aromatic	45.4 % (49 of 108)	87.0 % (47 of 54)	0.0 % (0 of 52)	100.0 % (2 of 2)
Methyl	100.0 % (76 of 76)	100.0 % (38 of 38)	100.0 % (38 of 38)

1. entity

MTRWVPTKRE EKYGVAFYNY DARGADELSL QIGDTVHILE TYEGWYRGYT LRKKSKKGIF PASYIHLKEA IVEG

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-100% 15N]		0.4 mM
2	PBS	natural abundance		50 mM
3	DTT	natural abundance		1 mM
4	EDTA	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
8	PBS	natural abundance		50 mM
9	DTT	natural abundance		1 mM
10	EDTA	natural abundance		1 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
13	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
14	PBS	natural abundance		50 mM
15	DTT	[U-100% 2H]		1 mM
16	EDTA	natural abundance		1 mM
17	D2O	natural abundance		100 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
18	SH3	natural abundance		0.4 mM
19	PBS	natural abundance		50 mM
20	DTT	[U-100% 2H]		1 mM
21	EDTA	natural abundance		1 mM
22	D2O	natural abundance		100 %

LACS Plot; CA

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; CB

Referencing offset: 0.11 ppm, Outliers: 1 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M0Y, Strand ID: A Detail

Release date

2012-08-11

Citation

Solution structure of the SH3 domain of DOCK180
Liu, X., Li, F., Pan, Z., Wang, W., Wen, W.
Proteins (2013), 81, 906-910, PubMed 23239367 , DOI 10.1002/prot.24236 , Abstract

Related entities 1. SH3 domain of DOCK180, : 1 : 5 : 106 entities Detail

Interaction partners 1. SH3 domain of DOCK180, : 11 interactors Detail

More details for 11 interactors identified by 3 citations

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-100% 15N]		0.4 mM
2	PBS	natural abundance		50 mM
3	DTT	natural abundance		1 mM
4	EDTA	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-100% 15N]		0.4 mM
2	PBS	natural abundance		50 mM
3	DTT	natural abundance		1 mM
4	EDTA	natural abundance		1 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-15N HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
8	PBS	natural abundance		50 mM
9	DTT	natural abundance		1 mM
10	EDTA	natural abundance		1 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

4 3D CBCA(CO)NH

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
8	PBS	natural abundance		50 mM
9	DTT	natural abundance		1 mM
10	EDTA	natural abundance		1 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

5 3D HNCACB

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
8	PBS	natural abundance		50 mM
9	DTT	natural abundance		1 mM
10	EDTA	natural abundance		1 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

6 3D HNCO

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
7	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
8	PBS	natural abundance		50 mM
9	DTT	natural abundance		1 mM
10	EDTA	natural abundance		1 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

7 2D 1H-13C HSQC

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
13	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
14	PBS	natural abundance		50 mM
15	DTT	[U-100% 2H]		1 mM
16	EDTA	natural abundance		1 mM
17	D2O	natural abundance		100 %

8 3D 1H-13C NOESY

Instrument

Varian VNMRS - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
13	SH3	[U-100% 13C; U-100% 15N]		0.4 mM
14	PBS	natural abundance		50 mM
15	DTT	[U-100% 2H]		1 mM
16	EDTA	natural abundance		1 mM
17	D2O	natural abundance		100 %

9 2D 1H-1H NOESY

Instrument

Varian VNMRS - 600 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
18	SH3	natural abundance		0.4 mM
19	PBS	natural abundance		50 mM
20	DTT	[U-100% 2H]		1 mM
21	EDTA	natural abundance		1 mM
22	D2O	natural abundance		100 %

10 2D 1H-1H TOCSY

Instrument

Varian VNMRS - 600 MHz

Sample

State anisotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
18	SH3	natural abundance		0.4 mM
19	PBS	natural abundance		50 mM
20	DTT	[U-100% 2H]		1 mM
21	EDTA	natural abundance		1 mM
22	D2O	natural abundance		100 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18832_2m0y.nef
Input source #2: Coordindates	2m0y.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----
MTRWVPTKREEKYGVAFYNYDARGADELSLQIGDTVHILETYEGWYRGYTLRKKSKKGIFPASYIHLKEAIVEG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MTRWVPTKREEKYGVAFYNYDARGADELSLQIGDTVHILETYEGWYRGYTLRKKSKKGIFPASYIHLKEAIVEG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	74	0	0	100.0

Content subtype: combined_18832_2m0y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shif	Warning	692		98.6 (chain: A, length: 74)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1639 (1)	noe	97.3 (chain: A, length: 74)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	32 (1)	hbond	24.3 (chain: A, length: 74)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	77 (77)	.	82.4 (chain: A, length: 74)

Assigned chemical shifts

Saveframe: assigned_chem_shif
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 98.6%
- Total number of assignments
  - ¹H chemical shifts: 419
  - ¹³C chemical shifts: 212
  - ¹⁵N chemical shifts: 61
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 97.3%
- Total number of restraints: 1638
- Weight of restraints: 1.0 (1638)
- Potential type of restraints: square-well-parabolic (1638)
- Range of distance target values: 2.19, 5.6 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 24.3%
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: square-well-parabolic (32)
  - Range of distance target values: 2.0, 2.75 (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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 74, Sequence coverage: 82.4%
- Total number of restraints: 77
- Total number of restraints per polymer type: 77
- Weight of restraints: 1.0 (77)
- Potential type of restraints: square-well-parabolic (77)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords DOCK180, SH3 domain