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BMRB: 16137

2KE7

NMR structure of the first SAM domain from AIDA1

Authors

Assembly

AIDA1

Entity

1. AIDA1 (polymer, Thiol state: all free), 103 monomers, 11490.92 Da Detail

GSDITSLYKK AGSEMNGPRC PVQTVGQWLE SIGLPQYENH LMANGFDNVQ FMGSNVMEDQ DLLEIGILNS GHRQRILQAI QLLPKMRPIG HDGYHPTSVA EWL

Formula weight

11490.92 Da

Source organism

Exptl. method

Refine. method

torsion angle dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 65.0 %, Completeness: 57.5 %, Completeness (bb): 61.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	57.5 % (688 of 1196)	56.5 % (353 of 625)	59.2 % (271 of 458)	56.6 % (64 of 113)
Backbone	61.4 % (372 of 606)	61.1 % (129 of 211)	60.4 % (180 of 298)	64.9 % (63 of 97)
Sidechain	53.8 % (367 of 682)	52.7 % (218 of 414)	58.7 % (148 of 252)	6.3 % (1 of 16)
Aromatic	40.5 % (34 of 84)	50.0 % (21 of 42)	30.0 % (12 of 40)	50.0 % (1 of 2)
Methyl	78.3 % (83 of 106)	75.5 % (40 of 53)	81.1 % (43 of 53)

1. AIDA1 SAM1

GSDITSLYKK AGSEMNGPRC PVQTVGQWLE SIGLPQYENH LMANGFDNVQ FMGSNVMEDQ DLLEIGILNS GHRQRILQAI QLLPKMRPIG HDGYHPTSVA EWL

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

LACS Plot; CA

Referencing offset: 0.27 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.27 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.36 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2KE7, Strand ID: A Detail

Release date

2015-07-23

Citation

NMR structure of the first SAM domain from AIDA1
Donaldson, L.
Not known

Related entities 1. AIDA1, : 1 : 2 : 37 entities Detail

Interaction partners 1. AIDA1, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

2 2D 1H-13C HSQC

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

3 3D CBCA(CO)NH

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

4 3D C(CO)NH

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

5 3D HNCO

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

6 3D HNCACB

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

7 3D H(CCO)NH

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

8 3D 1H-15N NOESY

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

9 3D 1H-13C NOESY

Instrument

Varian NMRS - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1.0 atm, Temperature 293 K, pH 7.8

#	Name	Isotope labeling	Type	Concentration
1	AIDA1 SAM1	[U-98% 13C; U-98% 15N]		0.8 mM
2	D2O	natural abundance		10 %
3	H2O	natural abundance		90 %
4	sodium chloride	natural abundance		150 mM
5	sodium phosphate	natural abundance		20 mM
6	sodium azide	natural abundance		0.05 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_16137_2ke7.nef
Input source #2: Coordindates	2ke7.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

------800-------810-------820-------830-------840-------850-------860-------870-------880-------890-
GSDITSLYKKAGSEMNGPRCPVQTVGQWLESIGLPQYENHLMANGFDNVQFMGSNVMEDQDLLEIGILNSGHRQRILQAIQLLPKMRPIGHDGYHPTSVA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSDITSLYKKAGSEMNGPRCPVQTVGQWLESIGLPQYENHLMANGFDNVQFMGSNVMEDQDLLEIGILNSGHRQRILQAIQLLPKMRPIGHDGYHPTSVA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

---
EWL
|||
EWL
---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	103	0	0	100.0

Content subtype: combined_16137_2ke7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assignments_aida3	Warning	651		61.2 (chain: A, length: 103)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	707 (1)	noe	57.3 (chain: A, length: 103)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	42 (1)	hbond	35.9 (chain: A, length: 103)

Assigned chemical shifts

Saveframe: assignments_aida3
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 61.2%
- Total number of assignments
  - ¹H chemical shifts: 333
  - ¹³C chemical shifts: 257
  - ¹⁵N chemical shifts: 61
- 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: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 57.3%
- Total number of restraints: 697
- Weight of restraints: 1.0 (697)
- Potential type of restraints: square-well-parabolic (697)
- Range of distance target values: 2.32, 3.63 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 103, Sequence coverage: 35.9%
  - Total number of restraints: 42
  - Weight of restraints: 1.0 (42)
  - Potential type of restraints: square-well-parabolic (42)
  - Range of distance target values: 1.9, 2.4 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Keywords SAM domain