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BMRB: 19033

2M51

NMR structure of the SH3 domain of human RAS p21 protein activator (GTPase activating protein) 1

Authors

Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.

Assembly

SH3 domain of human RAS GAP 1

Entity

1. SH3 domain of human RAS GAP 1 (polymer, Thiol state: not present), 62 monomers, 7259.151 Da Detail

GRRRVRAILP YTKVPDTDEI SFLKGDMFIV HNELEDGWMW VTNLRTDEQG LIVEDLVEEV GR

Formula weight

7259.151 Da

Source organism

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.4 %, Completeness: 89.4 %, Completeness (bb): 84.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.4 % (659 of 737)	96.6 % (370 of 383)	77.9 % (225 of 289)	98.5 % (64 of 65)
Backbone	84.5 % (311 of 368)	98.4 % (125 of 127)	70.2 % (127 of 181)	98.3 % (59 of 60)
Sidechain	94.8 % (404 of 426)	95.7 % (245 of 256)	93.3 % (154 of 165)	100.0 % (5 of 5)
Aromatic	80.4 % (45 of 56)	89.3 % (25 of 28)	69.2 % (18 of 26)	100.0 % (2 of 2)
Methyl	100.0 % (78 of 78)	100.0 % (39 of 39)	100.0 % (39 of 39)

1. RAS GAP 1

GRRRVRAILP YTKVPDTDEI SFLKGDMFIV HNELEDGWMW VTNLRTDEQG LIVEDLVEEV GR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 2.37 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: 2.37 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.06 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2M51, Strand ID: A Detail

Release date

2013-03-20

Citation

NMR structure of the SH3 domain of human RAS p21 protein activator (GTPase activating protein) 1
Dutta, S.K., Serrano, P., Geralt, M., Wuthrich, K.
Not known

Related entities 1. SH3 domain of human RAS GAP 1, : 1 : 12 : 157 entities Detail

Interaction partners 1. SH3 domain of human RAS GAP 1, : 3 interactors Detail

More details for 3 interactors identified by 2 citations

Experiments performed 7 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 4D-HACANH-APSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 5D-CBCACONH-APSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 5D-HACACONH-APSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.0

#	Name	Isotope labeling	Type	Concentration
1	RAS_GAP_1	[U-98% 13C; U-98% 15N]		1.2 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		50 mM
4	sodium azide	natural abundance		5 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_19033_2m51.nef
Input source #2: Coordindates	2m51.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--
GRRRVRAILPYTKVPDTDEISFLKGDMFIVHNELEDGWMWVTNLRTDEQGLIVEDLVEEVGR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GRRRVRAILPYTKVPDTDEISFLKGDMFIVHNELEDGWMWVTNLRTDEQGLIVEDLVEEVGR

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0

Content subtype: combined_19033_2m51.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	651		96.8 (chain: A, length: 62)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	1366 (1)	noe	96.8 (chain: A, length: 62)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 368
  - ¹³C chemical shifts: 214
  - ¹⁵N chemical shifts: 69
- Completeness of assignments
  - Entity_assemble_ID: A
- Peptide bond of PRO
- Tautomeric state of HIS
- 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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 96.8%
- Total number of restraints: 1366
- Weight of restraints: 1.0 (1366)
- Potential type of restraints: upper-bound-parabolic (1366)
- Range of distance target values: 2.72, 5.5 (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

Keywords SH3 domain of RAS GAP1