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BMRB: 17915

2LJ3

PFBD: High-throughput Strategy of Backbone fold Determination for small well-folded proteins in less than a day

Authors

Kumar, D.DR., Hosur, R.PROF.

Assembly

SH3

Entity

1. SH3 (polymer, Thiol state: not present), 62 monomers, 7219.162 Da Detail

MDETGKELVL ALYDYQEKSP REVTMKKGDI LTLLNSTNKD WWKVEVNDRQ GFVPAAYVKK LD

2. LL5 (non-polymer, Thiol state: not present), 334.436 × 5 Da

Total weight

8891.342 Da

Max. entity weight

7219.162 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.2 %, Completeness: 33.9 %, Completeness (bb): 64.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	33.9 % (256 of 755)	19.7 % (78 of 395)	40.6 % (119 of 293)	88.1 % (59 of 67)
Backbone	64.9 % (239 of 368)	50.4 % (63 of 125)	63.9 % (117 of 183)	98.3 % (59 of 60)
Sidechain	4.5 % (20 of 446)	5.6 % (15 of 270)	3.0 % (5 of 169)	0.0 % (0 of 7)
Aromatic	0.0 % (0 of 58)	0.0 % (0 of 29)	0.0 % (0 of 27)	0.0 % (0 of 2)
Methyl	2.9 % (2 of 70)	2.9 % (1 of 35)	2.9 % (1 of 35)

1. SH3

MDETGKELVL ALYDYQEKSP REVTMKKGDI LTLLNSTNKD WWKVEVNDRQ GFVPAAYVKK LD

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

Protein Blocks Logo

Calculated from 20 models in PDB: 2LJ3, Strand ID: A Detail

Release date

2011-10-06

Citation

Facile backbone (1H, 15N, 13Ca, and 13C') assignment of 13C/15N-labeled proteins using orthogonal projection planes of HNN and HN(C)N experiments and its automation
Kumar, D., Borkar, A., Hosur, R.V.
Magn. Reson. Chem. (2012), 50, 357-363, PubMed 22508472 , DOI 10.1002/mrc.3801 , Abstract

Related entities 1. SH3, : 1 : 11 : 2 : 36 : 272 entities Detail

Interaction partners 1. SH3, : 5 interactors Detail

More details for 5 interactors identified by 5 citations

Experiments performed 10 experiments Detail

1 2D hNcnH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

2 2D hncNH-G

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

3 2D hncNH-A

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

4 2D hncNH-ST

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

5 2D cbcacoNH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

6 2D HnCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

7 2D hnCOcanH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

8 2D-HncoCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

9 2D hncoCAnH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

10 2D-(HN)NH-G, A, ST

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 6.5 (±0.1)

#	Name	Isotope labeling	Type	Concentration
1	SH3	[U-99% 13C; U-99% 15N]		1.2 mM
2	sodium phosphate	natural abundance		50 (±0.05) mM
3	NaCl	natural abundance		150 (±0.05) mM
4	H2O	natural abundance		90 (±0.05) %
5	D2O	natural abundance		10 (±0.05) %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17915_2lj3.nef
Input source #2: Coordindates	2lj3.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	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:62:ASP:C	1:63:NH2:N	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	90	NH2	AMINO GROUP	Coordinates

Sequence alignments

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

--------10--------20--------30--------40--------50--------60-90
MDETGKELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLDX
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MDETGKELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLDX
--------10--------20--------30--------40--------50--------60---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	63	0	0	100.0

Content subtype: combined_17915_2lj3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	OK	232		93.7 (chain: A, length: 63)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	230 (1)	noe	93.7 (chain: A, length: 63)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	76 (76)	.	84.1 (chain: A, length: 63)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: OK
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 93.7%
- Total number of assignments
  - ¹H chemical shifts: 59
  - ¹³C chemical shifts: 114
  - ¹⁵N chemical shifts: 59
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 93.7%
- Total number of restraints: 230
- Weight of restraints: 1.0 (230)
- Potential type of restraints: upper-bound-parabolic (230)
- Range of distance target values: 5.0, 6.5 (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_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 63, Sequence coverage: 84.1%
- Total number of restraints: 76
- Total number of restraints per polymer type: 76
- Weight of restraints: 1.0 (76)
- Potential type of restraints: square-well-parabolic (76)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Chicken SH3 Domain