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Found 1 Document (1.216 seconds)

BMRB: 17629

2LCS

Yeast Nbp2p SH3 domain in complex with a peptide from Ste20p

Authors

Gorelik, M., Davidson, A.R.

Assembly

Nbp2 SH3 and Ste20 peptide

Entity

1. Nbp2 SH3 (polymer, Thiol state: not present), 73 monomers, 8380.115 Da Detail

MAIVNQRAVA LYDFEPENDN ELRLAEGDIV FISYKHGQGW LVAENESGSK TGLVPEEFVS YIQPELEHHH HHH

2. Ste20 peptide (polymer, Thiol state: not present), 16 monomers, 1636.890 Da Detail

GKFIPSRPAP KPPSSA

Total weight

10017.005 Da

Max. entity weight

8380.115 Da

Source organism

Saccharomyces cerevisiae

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.0 %, Completeness: 80.2 %, Completeness (bb): 79.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	80.2 % (831 of 1036)	88.0 % (475 of 540)	69.5 % (283 of 407)	82.0 % (73 of 89)
Backbone	79.7 % (413 of 518)	89.2 % (157 of 176)	73.2 % (191 of 261)	80.2 % (65 of 81)
Sidechain	79.4 % (477 of 601)	87.4 % (318 of 364)	65.9 % (151 of 229)	100.0 % (8 of 8)
Aromatic	57.7 % (60 of 104)	71.2 % (37 of 52)	43.1 % (22 of 51)	100.0 % (1 of 1)
Methyl	90.5 % (76 of 84)	92.9 % (39 of 42)	88.1 % (37 of 42)

1. Nbp2 SH3

MAIVNQRAVA LYDFEPENDN ELRLAEGDIV FISYKHGQGW LVAENESGSK TGLVPEEFVS YIQPELEHHH HHH

2. Ste20 peptide

GKFIPSRPAP KPPSSA

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
8	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
9	Ste20 peptide	natural abundance	1.4 (±0.1) mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	50 mM
12	sodium azide	natural abundance	0.05 %
13	D2O	natural abundance	100 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
14	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
15	Ste20 peptide	natural abundance	0.7 (±0.1) mM
16	sodium chloride	natural abundance	100 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium azide	natural abundance	0.05 %
19	D2O	natural abundance	5 %
20	H2O	natural abundance	95 %

Sample #4

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
21	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
22	Ste20 peptide	natural abundance	0.7 (±0.1) mM
23	sodium chloride	natural abundance	100 mM
24	sodium phosphate	natural abundance	50 mM
25	sodium azide	natural abundance	0.05 %
26	D2O	natural abundance	100 %

Protein Blocks Logo

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

Release date

2011-06-02

Citation

Not known
Gorelik, M., Davidson, A.R.
Not known

Related entities 1. Nbp2 SH3, : 1 : 36 entities Detail

Related entities 2. Ste20 peptide, : 1 : 4 : 6 entities Detail

Interaction partners 2. Ste20 peptide, : 36 interactors Detail

More details for 36 interactors identified by 16 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

2 3D CBCA(CO)NH

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

3 3D HNCACB

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

4 3D HNCO

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

5 3D HN(CO)CA

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

6 3D C(CO)NH

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

7 3D H(CCO)NH

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
1	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
2	Ste20 peptide	natural abundance	1.4 (±0.1) mM
3	sodium chloride	natural abundance	100 mM
4	sodium phosphate	natural abundance	50 mM
5	sodium azide	natural abundance	0.05% %
6	D2O	natural abundance	5% %
7	H2O	natural abundance	95% %

8 3D HCCH-COSY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
8	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
9	Ste20 peptide	natural abundance	1.4 (±0.1) mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	50 mM
12	sodium azide	natural abundance	0.05 %
13	D2O	natural abundance	100 %

9 3D 1H-15N NOESY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
8	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
9	Ste20 peptide	natural abundance	1.4 (±0.1) mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	50 mM
12	sodium azide	natural abundance	0.05 %
13	D2O	natural abundance	100 %

10 3D 1H-13C NOESY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
8	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
9	Ste20 peptide	natural abundance	1.4 (±0.1) mM
10	sodium chloride	natural abundance	100 mM
11	sodium phosphate	natural abundance	50 mM
12	sodium azide	natural abundance	0.05 %
13	D2O	natural abundance	100 %

11 N15 C13 filtered 2D 1H-1H TOCSY

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
14	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
15	Ste20 peptide	natural abundance	0.7 (±0.1) mM
16	sodium chloride	natural abundance	100 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium azide	natural abundance	0.05 %
19	D2O	natural abundance	5 %
20	H2O	natural abundance	95 %

12 15N C13 filtered 2D 1H-1H NOESY

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
14	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
15	Ste20 peptide	natural abundance	0.7 (±0.1) mM
16	sodium chloride	natural abundance	100 mM
17	sodium phosphate	natural abundance	50 mM
18	sodium azide	natural abundance	0.05 %
19	D2O	natural abundance	5 %
20	H2O	natural abundance	95 %

13 13C half-filtered 3D 1H-13C NOESY

Instrument

Bruker INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
21	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
22	Ste20 peptide	natural abundance	0.7 (±0.1) mM
23	sodium chloride	natural abundance	100 mM
24	sodium phosphate	natural abundance	50 mM
25	sodium azide	natural abundance	0.05 %
26	D2O	natural abundance	100 %

14 13C filtered 2D 1H-1H COSY

Instrument

Bruker INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.8

#	Name	Isotope labeling	Concentration
21	Nbp2 SH3	[U-99% 13C; U-99% 15N]	0.7 (±0.1) mM
22	Ste20 peptide	natural abundance	0.7 (±0.1) mM
23	sodium chloride	natural abundance	100 mM
24	sodium phosphate	natural abundance	50 mM
25	sodium azide	natural abundance	0.05 %
26	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17629_2lcs.nef
Input source #2: Coordindates	2lcs.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	Error

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	0	.	Not matched with CCD	None

Sequence alignments

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

----------------
GKFIPSRPAPKPPSSA
||||||||||||||||
GKFIPSRPAPKPPSSA
--------10------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	73	1	0	100.0
B	B	16	0	0	100.0

Content subtype: combined_17629_2lcs.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift__list_1	Warning	833		93.8 (chain: B, length: 16)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	2531 (1)	noe	68.8 (chain: B, length: 16)
2	Distance restraints	DYANA/DIANA_distance_constraints_3	Error	32 (1)	hbond	No information
3	Distance restraints	DYANA/DIANA_distance_constraints_4	Error	32 (1)	hbond	No information
1	Dihedral angle restraints	DYANA/DIANA_dihedral_5	Warning	87 (87)	.	12.5 (chain: B, length: 16)

Assigned chemical shifts

Saveframe: assigned_chem_shift__list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 93.8%
- Total number of assignments
  - ¹H chemical shifts: 482
  - ¹³C chemical shifts: 280
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: B
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: B

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	90	89.1
¹³C chemical shifts	73	0	0.0
¹⁵N chemical shifts	12	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	28	24	85.7
¹³C chemical shifts	32	0	0.0
¹⁵N chemical shifts	11	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	66	90.4
¹³C chemical shifts	41	0	0.0
¹⁵N chemical shifts	1	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	4	4	100.0
¹³C chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	5	4	80.0
¹³C chemical shifts	5	0	0.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 68.8%
- Total number of restraints: 2531
- Weight of restraints: 1.0 (2531)
- Potential type of restraints: upper-bound-parabolic (2531)
- Range of distance target values: 2.4, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_3
  - Status: Error
  - Experiment type: hbond
  - Total number of restraints: 32
  - Weight of restraints: 1.0 (32)
  - Potential type of restraints: upper-bound-parabolic (32)
  - Range of distance target values: 2.0, 3.0 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: DYANA/DIANA_distance_constraints_4
    - Status: Error
    - Experiment type: hbond
    - Total number of restraints: 32
    - Weight of restraints: 1.0 (32)
    - Potential type of restraints: upper-bound-parabolic (32)
    - Range of distance target values: 1.8, 2.7 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_5
- Status: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: B, Chain length: 16, Sequence coverage: 12.5%
- Total number of restraints: 87
- Total number of restraints per polymer type: 87
- Weight of restraints: 1.0 (87)
- Potential type of restraints: square-well-parabolic (87)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords complex, Nbp2p, peptide, SH3, Ste20p

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Found 1 Document (1.216 seconds)

BMRB: 17629

Sample #1

Sample #2

Sample #3

Sample #4

Related entities 1. Nbp2 SH3, : 1 : 36 entities Detail

Related entities 2. Ste20 peptide, : 1 : 4 : 6 entities Detail

Interaction partners 2. Ste20 peptide, : 36 interactors Detail

Experiments performed 14 experiments Detail

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NMR combined restraints 6 contents Detail