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)
1:17:CYS:SG	2:1:HEC:CAC	unknown	unknown	n/a
1:14:CYS:SG	2:1:HEC:CAB	unknown	unknown	n/a
1:18:HIS:NE2	2:1:HEC:FE	unknown	unknown	n/a
1:80:MET:SD	2:1:HEC:FE	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	HEC	HEME C	Assigned chemical shifts

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

----
ATNE
||||
ATNE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	104	0	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	assigned_chem_shift_list_1	Error	1093		99.0 (chain: A, length: 104), 100.0 (chain: B, length: 1)
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: assigned_chem_shift_list_1
- Status: Error
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 99.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 594
  - ¹³C chemical shifts: 396
  - ¹⁵N chemical shifts: 103
- Completeness of assignments
  - Entity_assemble_ID: B
- 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

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	12	54.5
¹³C chemical shifts	34	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	12	54.5
¹³C chemical shifts	34	0	0.0
¹⁵N chemical shifts	4	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	6	5	83.3
¹³C chemical shifts	6	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	16	0	0.0
¹⁵N chemical shifts	4	0	0.0

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

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.989 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

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 5 contents Detail