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BMRB: 25395

2MX7

Solution structure of the internal EH domain of gamma-synergin

Authors

Kovermann, M., Weininger, U., Loew, C.

Assembly

internal EH domain of gamma-synergin

Entity

1. internal EH domain of gamma-synergin (polymer, Thiol state: not present), 112 monomers, 12285.19 Da Detail

SMFPSQDPAQ PRMPPWIYNE SLVPDAYKKI LETTMTPTGI DTAKLYPILM SSGLPRETLG QIWALANRTT PGKLTKEELY TVLAMIAVTQ RGVPAMSPDA LNQFPAAPIP TL

Formula weight

12285.19 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.4 %, Completeness: 84.2 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.2 % (1099 of 1306)	91.5 % (622 of 680)	75.1 % (390 of 519)	81.3 % (87 of 107)
Backbone	81.8 % (525 of 642)	89.7 % (192 of 214)	77.3 % (256 of 331)	79.4 % (77 of 97)
Sidechain	87.0 % (671 of 771)	92.3 % (430 of 466)	78.3 % (231 of 295)	100.0 % (10 of 10)
Aromatic	60.5 % (46 of 76)	100.0 % (38 of 38)	16.7 % (6 of 36)	100.0 % (2 of 2)
Methyl	95.7 % (132 of 138)	95.7 % (66 of 69)	95.7 % (66 of 69)

1. entity

SMFPSQDPAQ PRMPPWIYNE SLVPDAYKKI LETTMTPTGI DTAKLYPILM SSGLPRETLG QIWALANRTT PGKLTKEELY TVLAMIAVTQ RGVPAMSPDA LNQFPAAPIP TL

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

LACS Plot; CA

Referencing offset: -0.18 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.18 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: 0.28 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.15 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MX7, Strand ID: A Detail

Release date

2015-12-27

Citation

Solution structure of the internal EH domain of gamma-synergin
Kovermann, M., Weininger, U., Loew, C.
Not known

Related entities 1. internal EH domain of gamma-synergin, : 17 entities Detail

Interaction partners 1. internal EH domain of gamma-synergin, : 8 interactors Detail

More details for 8 interactors identified by 5 citations

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

3 2D 1H-1H TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

4 2D 1H-1H NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

5 3D 1H-15N NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

6 3D 1H-13C NOESY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

7 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

8 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

9 3D HNCACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

10 3D HN(CO)CACB

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

12 2D 1H-15N HSQC IPAP

Instrument

Bruker Avance - 850 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		1 mM
2	TRIS	natural abundance		20 mM
3	sodium chloride	natural abundance		100 mM
4	calcium chloride	natural abundance		2 mM

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints, RDC restraints	combined_25395_2mx7.nef
Input source #2: Coordindates	2mx7.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

---280-----290-------300-------310-------320-------330-------340-------350-------360-------370------
SMFPSQDPAQPRMPPWIYNESLVPDAYKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGKLTKEELYTVLAMIAVTQRGVPAMSPDA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SMFPSQDPAQPRMPPWIYNESLVPDAYKKILETTMTPTGIDTAKLYPILMSSGLPRETLGQIWALANRTTPGKLTKEELYTVLAMIAVTQRGVPAMSPDA
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-380--------
LNQFPAAPIPTL
||||||||||||
LNQFPAAPIPTL
-------110--

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	112	0	0	100.0

Content subtype: combined_25395_2mx7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1100		96.4 (chain: A, length: 112)
1	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	59 (1)	hbond	41.1 (chain: A, length: 112)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_2	OK	185 (185)	.	99.1 (chain: A, length: 112)
1	RDC restraints	CNS/XPLOR_dipolar_coupling_5	OK	44 (44)	.	39.3 (chain: A, length: 112)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 96.4%
- Total number of assignments
  - ¹H chemical shifts: 632
  - ¹³C chemical shifts: 382
  - ¹⁵N chemical shifts: 86
- 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_4
- Status: OK
- Experiment type: hbond
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 41.1%
- Total number of restraints: 59
- Weight of restraints: 1.0 (59)
- Potential type of restraints: square-well-parabolic (59)
- Range of distance target values: 2.05, 3.05 (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_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 99.1%
- Total number of restraints: 185
- Total number of restraints per polymer type: 185
- Weight of restraints: 1.0 (185)
- Potential type of restraints: square-well-parabolic (185)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

RDC restraints

Saveframe: CNS/XPLOR_dipolar_coupling_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 112, Sequence coverage: 39.3%
- Total number of restraints: 44
- Potential type of restraints: undefined (44)
- Range of observed RDC values: 100.0, -100.0 (Hz)
- RDC restraints per residue

Keywords EF hand, EH domain, NPF repeat