BMRBj - BMREntryMaster

	Total	¹H	¹³C	¹⁵N
All	86.3 % (1077 of 1248)	86.2 % (570 of 661)	84.1 % (403 of 479)	96.3 % (104 of 108)
Backbone	94.6 % (577 of 610)	94.4 % (202 of 214)	93.6 % (278 of 297)	98.0 % (97 of 99)
Sidechain	80.5 % (587 of 729)	82.3 % (368 of 447)	77.7 % (212 of 273)	77.8 % (7 of 9)
Aromatic	30.4 % (28 of 92)	45.7 % (21 of 46)	13.3 % (6 of 45)	100.0 % (1 of 1)
Methyl	97.8 % (90 of 92)	95.7 % (44 of 46)	100.0 % (46 of 46)

1. entity 1

GDVEKGKKIF VQKCAQCXTV EKGGKHKTGP NLHGLFGRKT GQAPGFTYTD ANKNKGITWK EETLMEYLEN PKKYIPGTKM IFAGIKKKTE REDLIAYLKK ATNEX

Show sample condition

Sample #1

Solvent system Deuterated pentane, Pressure 1 atm, Temperature 298 K, pH 7.4, Details Aqueous cytochrome c was encapsulated in reverse micelles composed of 1-decanoyl-rac-glycerol (10MAG) and lauryldimethylamine-N-oxide (LDAO), with trace amounts of hexanol.

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

Sample #2

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 15N]	0.15 mM
9	H2O	natural abundance	1.5 M
10	sodium phosphate	natural abundance	25 mM
11	1-decanoyl-rac-glycerol	natural abundance	105 mM
12	lauryldimethylamine-N-oxide	natural abundance	45 mM
13	hexanol	natural abundance	8 mM
14	pentane	[U-99% 2H]	8.67 M

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: -0.84 ppm, Outliers: 1 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: -0.84 ppm, Outliers: 1 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: 0.06 ppm, Outliers: 3 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: -0.68 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 32 models in PDB: 2N3B, Strand ID: A Detail

Release date

2015-10-25

Citation

Defining the apoptotic trigger: the interaction of cytochrome c and cardiolipin
O'Brien, E.S., Nucci, N.V., Fuglestad, B., Tommos, C., Wand, A.
J. Biol. Chem. (2015), 290, 30879-30887, PubMed 26487716 , DOI 10.1074/jbc.M115.689406 , Abstract

Related entities 1. INTERACTION OF CYTOCHROME C AND CARDIOLIPIN, entity 1, : 1 : 31 : 209 entities Detail

Interaction partners 1. INTERACTION OF CYTOCHROME C AND CARDIOLIPIN, entity 1, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system Deuterated pentane, Pressure 1 atm, Temperature 298 K, pH 7.4, Details Aqueous cytochrome c was encapsulated in reverse micelles composed of 1-decanoyl-rac-glycerol (10MAG) and lauryldimethylamine-N-oxide (LDAO), with trace amounts of hexanol.

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

3 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

4 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

6 3D H(CCO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

7 3D C(CO)NH

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

8 3D 1H-15N NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

9 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

10 4D 1H-15N-13C-1H NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

11 3D HNCO

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	entity_1	[U-100% 13C; U-100% 15N]	0.15 mM
2	H2O	natural abundance	1.5 M
3	sodium phosphate	natural abundance	25 mM
4	1-decanoyl-rac-glycerol	natural abundance	105 mM
5	lauryldimethylamine-N-oxide	natural abundance	45 mM
6	hexanol	natural abundance	8 mM
7	pentane	[U-99% 2H]	8.67 M

12 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 15N]	0.15 mM
9	H2O	natural abundance	1.5 M
10	sodium phosphate	natural abundance	25 mM
11	1-decanoyl-rac-glycerol	natural abundance	105 mM
12	lauryldimethylamine-N-oxide	natural abundance	45 mM
13	hexanol	natural abundance	8 mM
14	pentane	[U-99% 2H]	8.67 M

13 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
8	entity_1	[U-100% 15N]	0.15 mM
9	H2O	natural abundance	1.5 M
10	sodium phosphate	natural abundance	25 mM
11	1-decanoyl-rac-glycerol	natural abundance	105 mM
12	lauryldimethylamine-N-oxide	natural abundance	45 mM
13	hexanol	natural abundance	8 mM
14	pentane	[U-99% 2H]	8.67 M

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25640_2n3b.nef
Input source #2: Coordindates	2n3b.cif
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:17:CYS:SG	A:201:HEC:CAC	oxidized, CA 58.348, CB 36.453 ppm	unknown	n/a
A:14:CYS:SG	A:201:HEC:CAB	oxidized, CA 55.043, CB 37.82 ppm	unknown	n/a
A:18:HIS:NE2	A:201:HEC:FE	unknown	unknown	n/a
A:80:MET:SD	A:201:HEC:FE	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	201	HEC	HEME C	Assigned chemical shifts
B	1	HOH	WATER	None
C	1	HOH	WATER	None
D	1	HOH	WATER	None
E	1	HOH	WATER	None

Sequence alignments

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDVEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGFTYTDANKNKGITWKEETLMEYLENPKKYIPGTKMIFAGIKKKTEREDLIAYLKK
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

-----
ATNEX
|||| 
ATNE 
----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	1	0	100.0

Content subtype: combined_25640_2n3b.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	nef_chemical_shift_list_assigned_chem_shift_list_1	Error	988		99.0 (chain: A, length: 105)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	2350 (1)	noe	100.0 (chain: A, length: 104)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	57 (1)	hbond	67.3 (chain: A, length: 104)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	145 (145)	.	92.3 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: nef_chemical_shift_list_assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 105, Sequence coverage: 99.0%
- Total number of assignments
  - ¹H chemical shifts: 489
  - ¹³C chemical shifts: 396
  - ¹⁵N chemical shifts: 103
- Completeness of assignments
- Redox state of CYS
- 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

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of restraints: 2342
- Weight of restraints: 1.0 (2342)
- Potential type of restraints: square-well-parabolic (2342)
- Range of distance target values: 2.35, 5.6 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- 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: 104, Sequence coverage: 67.3%
  - Total number of restraints: 57
  - Weight of restraints: 1.0 (57)
  - Potential type of restraints: square-well-parabolic (57)
  - Range of distance target values: 2.1, 2.2 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 92.3%
- Total number of restraints: 145
- Total number of restraints per polymer type: 145
- Weight of restraints: 1.0 (145)
- Potential type of restraints: square-well-parabolic (145)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cytochrome c, paramagnetic, reverse micelle, structural water

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Found 1 Document (1.925 seconds)

BMRB: 25640

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. INTERACTION OF CYTOCHROME C AND CARDIOLIPIN, entity 1, : 1 : 31 : 209 entities Detail

Interaction partners 1. INTERACTION OF CYTOCHROME C AND CARDIOLIPIN, entity 1, : 1 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail