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Found 1 Document (0.944 seconds)

BMRB: 18464

2LT9

The solution structure of Ca2+ binding domain 2B of the third isoform of the Na+/Ca2+ exchanger

Authors

Breukels, V., Touw, W.G., Vuister, G.W.

Assembly

NCX3

Entity

1. NCX3 (polymer, Thiol state: not present), 157 monomers, 17871.79 Da Detail

MASHHHHHHH AGIFTFECDT IHVSESIGVM EVKVLRTSGA RGTVIVPFRT VEGTAKGGGE DFEDAYGELE FKNDETVKTI RVKIVDEEEY ERQENFFIAL GEPKWMERGI SEVTDRKLTV EEEEAKRIAE MGKPVLGEHP KLEVIIEESY EFKSTVD

Formula weight

17871.79 Da

Source organism

Mus musculus

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 91.1 %, Completeness: 81.9 %, Completeness (bb): 87.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	81.9 % (1487 of 1816)	81.1 % (763 of 941)	81.6 % (586 of 718)	87.9 % (138 of 157)
Backbone	87.0 % (813 of 934)	89.2 % (288 of 323)	85.4 % (391 of 458)	87.6 % (134 of 153)
Sidechain	78.4 % (804 of 1026)	77.0 % (476 of 618)	80.2 % (324 of 404)	100.0 % (4 of 4)
Aromatic	52.0 % (79 of 152)	53.9 % (41 of 76)	49.3 % (37 of 75)	100.0 % (1 of 1)
Methyl	97.0 % (161 of 166)	96.4 % (80 of 83)	97.6 % (81 of 83)

1. NCX3

MASHHHHHHH AGIFTFECDT IHVSESIGVM EVKVLRTSGA RGTVIVPFRT VEGTAKGGGE DFEDAYGELE FKNDETVKTI RVKIVDEEEY ERQENFFIAL GEPKWMERGI SEVTDRKLTV EEEEAKRIAE MGKPVLGEHP KLEVIIEESY EFKSTVD

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	NCX3	[U-100% 15N]	0.5 (±0.1) mM
8	HEPES	natural abundance	20 (±0.1) mM
9	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
10	CaCl2	natural abundance	10 (±0.1) mM
11	Pf1 phage	natural abundance	8 (±0.5) mg/mL
12	H2O	natural abundance	95 (±0.1) %
13	D2O	natural abundance	5 (±0.1) %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
14	NCX3	[U-100% 15N]	0.5 (±0.1) mM
15	HEPES	natural abundance	20 (±0.1) mM
16	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
17	CaCl2	natural abundance	10 (±0.1) mM
18	H2O	natural abundance	95 (±0.1) %
19	D2O	natural abundance	5 (±0.1) %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.1 ppm, Outliers: 2 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.11 ppm, Outliers: 2 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.07 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LT9, Strand ID: A Detail

Release date

2012-07-29

Citation

NMR structure note: solution structure of Ca²⁺ binding domain 2B of the third isoform of the Na⁺/Ca²⁺ exchanger
Breukels, V., Touw, W.G., Vuister, G.W.
J. Biomol. NMR (2012), 54, 115-121, PubMed 22806131 , DOI 10.1007/s10858-012-9654-1 , Abstract

Related entities 1. NCX3, : 1 : 45 entities Detail

Interaction partners 1. NCX3, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

2 3D HNCO

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

3 3D HNCACB

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

6 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

7 3D HNHA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

8 2D 1H-15N IPAP HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State anisotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
7	NCX3	[U-100% 15N]	0.5 (±0.1) mM
8	HEPES	natural abundance	20 (±0.1) mM
9	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
10	CaCl2	natural abundance	10 (±0.1) mM
11	Pf1 phage	natural abundance	8 (±0.5) mg/mL
12	H2O	natural abundance	95 (±0.1) %
13	D2O	natural abundance	5 (±0.1) %

9 2D 1H-13C IPAP HSQC

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
14	NCX3	[U-100% 15N]	0.5 (±0.1) mM
15	HEPES	natural abundance	20 (±0.1) mM
16	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
17	CaCl2	natural abundance	10 (±0.1) mM
18	H2O	natural abundance	95 (±0.1) %
19	D2O	natural abundance	5 (±0.1) %

10 3D 1H-13C NOESY aliphatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

11 3D 1H-13C NOESY aromatic

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

13 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 306 (±1) K, pH 7.0 (±0.1)

#	Name	Isotope labeling	Concentration
1	NCX3	[U-100% 13C; U-100% 15N]	0.5 (±0.1) mM
2	HEPES	natural abundance	20 (±0.1) mM
3	beta-mercaptoethanol	natural abundance	20 (±0.1) mM
4	CaCl2	natural abundance	10 (±0.1) mM
5	H2O	natural abundance	95 (±0.1) %
6	D2O	natural abundance	5 (±0.1) %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18464_2lt9.nef
Input source #2: Coordindates	2lt9.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

-520-----530-------540-------550-------560-------570-------580-------590-------600-------610-------6
MASHHHHHHHAGIFTFECDTIHVSESIGVMEVKVLRTSGARGTVIVPFRTVEGTAKGGGEDFEDAYGELEFKNDETVKTIRVKIVDEEEYERQENFFIAL
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MASHHHHHHHAGIFTFECDTIHVSESIGVMEVKVLRTSGARGTVIVPFRTVEGTAKGGGEDFEDAYGELEFKNDETVKTIRVKIVDEEEYERQENFFIAL
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

20-------630-------640-------650-------660-------670-----
GEPKWMERGISEVTDRKLTVEEEEAKRIAEMGKPVLGEHPKLEVIIEESYEFKSTVD
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GEPKWMERGISEVTDRKLTVEEEEAKRIAEMGKPVLGEHPKLEVIIEESYEFKSTVD
-------110-------120-------130-------140-------150-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	157	0	0	100.0

Content subtype: combined_18464_2lt9.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1444		87.9 (chain: A, length: 157)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	3794 (1)	noe	87.3 (chain: A, length: 157)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	186 (186)	.	77.7 (chain: A, length: 157)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 87.9%
- Total number of assignments
  - ¹H chemical shifts: 737
  - ¹³C chemical shifts: 572
  - ¹⁵N chemical shifts: 135
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	941	737	78.3
¹³C chemical shifts	718	572	79.7
¹⁵N chemical shifts	165	135	81.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	323	280	86.7
¹³C chemical shifts	314	254	80.9
¹⁵N chemical shifts	153	131	85.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	618	457	73.9
¹³C chemical shifts	404	318	78.7
¹⁵N chemical shifts	12	4	33.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	82	94.3
¹³C chemical shifts	87	83	95.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	38	50.0
¹³C chemical shifts	75	37	49.3
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 87.3%
- Total number of restraints: 3794
- Weight of restraints: 1.0 (3794)
- Potential type of restraints: upper-bound-parabolic (3794)
- Range of distance target values: 2.2, 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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 77.7%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords calcium binding domain 2, CBD, CBD2, NaCa exchanger, NCX, NCX3

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Found 1 Document (0.944 seconds)

BMRB: 18464

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. NCX3, : 1 : 45 entities Detail

Interaction partners 1. NCX3, : 1 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 4 contents Detail