BMRBj - BMREntryMaster

Found 1 Document (1.137 seconds)

BMRB: 25907

2N9I

solution structure of reduced human cytochrome c

Authors

Imai, M., Saio, T., Kumeta, H., Uchida, T., Inagaki, F., Ishimori, K.

Assembly

reduced human cytochrome c

Entity

1. Cyt c (polymer, Thiol state: all other bound), 104 monomers, 11617.39 Da Detail

GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE

2. HEME C (non-polymer), 618.503 Da

Total weight

12235.893 Da

Max. entity weight

11617.39 Da

Entity Connection

thioether 2 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	thioether	sing	1:CYS14:SG	2:HEC1:CAB
2	thioether	sing	1:CYS17:SG	2:HEC1:CAC

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 98.2 %, Completeness (bb): 98.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	98.2 % (1230 of 1252)	99.5 % (659 of 662)	96.5 % (465 of 482)	98.1 % (106 of 108)
Backbone	98.1 % (604 of 616)	99.5 % (216 of 217)	97.0 % (290 of 299)	98.0 % (98 of 100)
Sidechain	98.6 % (717 of 727)	99.6 % (443 of 445)	97.1 % (266 of 274)	100.0 % (8 of 8)
Aromatic	89.4 % (84 of 94)	95.7 % (45 of 47)	82.6 % (38 of 46)	100.0 % (1 of 1)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. Cyt c

GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSYTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N9I, Strand ID: A Detail

Release date

2016-02-14

Citation

Investigation of the redox-dependent modulation of structure and dynamics in human cytochrome c
Imai, M., Saio, T., Kumeta, H., Uchida, T., Inagaki, F., Ishimori, K.
Biochem. Biophys. Res. Commun. (2016), 469, 978-984, PubMed 26718409 , DOI 10.1016/j.bbrc.2015.12.079 , Abstract

Related entities 1. Cyt c, : 1 : 5 : 3 : 8 : 219 entities Detail

Interaction partners 1. Cyt c, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 20 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

2 2D 1H-13C HSQC aliphatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

3 2D 1H-13C HSQC aromatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

4 2D 1H-1H NOESY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
5	Cyt c	natural abundance	protein	1 mM
6	sodium phosphate	natural abundance		50 mM
7	D2O	[U-2H]	solvent	100 %

5 3D CBCA(CO)NH

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

6 3D C(CO)NH

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

7 3D HNCO

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

8 3D HNCACB

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

9 3D HBHA(CO)NH

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

10 3D HN(CO)CA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

11 3D H(CCO)NH

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

12 3D 1H-15N NOESY

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

13 3D 1H-13C NOESY aliphatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

14 3D 1H-13C NOESY aromatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

15 3D HNCA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

16 3D HNCAHA

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

17 3D HCCH TOCSY aliphatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

18 3D HCCH TOCSY aromatic

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

19 HbCbCgCdHd

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

20 HbCbCgCdCeHe

Instrument

Agilent INOVA - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8

#	Name	Isotope labeling	Type	Concentration
1	Cyt c	[U-99% 13C; U-99% 15N]	protein	0.5 ~ 1.0 mM
2	sodium phosphate	natural abundance	buffer	50 mM
3	H2O	natural abundance	solvent	95 %
4	D2O	[U-2H]	solvent	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25907_2n9i.nef
Input source #2: Coordindates	2n9i.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	Warning

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

----
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_25907_2n9i.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	Warning	1256		100.0 (chain: A, length: 104), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2579 (1)	noe	100.0 (chain: A, length: 104)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	58 (58)	.	76.9 (chain: A, length: 104)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 682
  - ¹³C chemical shifts: 466
  - ¹⁵N chemical shifts: 108
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
18	HIS	HD1	9.652
18	HIS	ND1	129.987
38	ARG	HH11	6.725
38	ARG	CZ	184.497
40	THR	HG1	4.887
48	TYR	HH	9.551
49	THR	HG1	8.785
54	ASN	CG	176.916
63	THR	HG1	4.616
78	THR	HG1	8.486
103	ASN	CG	177.707

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	662	658	99.4
¹³C chemical shifts	482	463	96.1
¹⁵N chemical shifts	110	107	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	217	215	99.1
¹³C chemical shifts	208	199	95.7
¹⁵N chemical shifts	100	97	97.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	445	443	99.6
¹³C chemical shifts	274	264	96.4
¹⁵N chemical shifts	10	10	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	50	50	100.0
¹³C chemical shifts	50	50	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	45	95.7
¹³C chemical shifts	46	36	78.3
¹⁵N chemical shifts	1	1	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	17	77.3
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	17	77.3
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	6	100.0
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: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 100.0%
- Total number of restraints: 2579
- Weight of restraints: 1.0 (2579)
- Potential type of restraints: upper-bound-parabolic (2579)
- Range of distance target values: 2.27, 5.5 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 76.9%
- Total number of restraints: 58
- Total number of restraints per polymer type: 58
- Weight of restraints: 1.0 (58)
- Potential type of restraints: square-well-parabolic (58)
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords cytochrome c, electron transfer

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Found 1 Document (1.137 seconds)

BMRB: 25907

Sample

Related entities 1. Cyt c, : 1 : 5 : 3 : 8 : 219 entities Detail

Interaction partners 1. Cyt c, : 1 interactors Detail

Experiments performed 20 experiments Detail

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NMR combined restraints 4 contents Detail