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BMRB: 25660

2N3Y

NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state

Authors

Moreno-Beltran, B., Del Conte, R., Diaz-Quintana, A., De la Rosa, M.A., Turano, P., Diaz-Moreno, I.

Assembly

Y48pCMF variant of human cytochrome c in its reduced state

Entity

1. Y48pCMF variant of human cytochrome c in its reduced state, entity (polymer), 104 monomers, 11882.74 Da Detail

GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSXTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE

2. PROTOPORPHYRIN IX CONTAINING FE (non-polymer), 616.487 Da

Total weight

12499.228 Da

Max. entity weight

11882.74 Da

Source organism

Exptl. method

Refine. method

distance geometry, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.0 %, Completeness: 92.9 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.9 % (1148 of 1236)	95.9 % (627 of 654)	89.5 % (425 of 475)	89.7 % (96 of 107)
Backbone	96.2 % (587 of 610)	96.3 % (207 of 215)	98.3 % (291 of 296)	89.9 % (89 of 99)
Sidechain	90.8 % (650 of 716)	95.7 % (420 of 439)	82.9 % (223 of 269)	87.5 % (7 of 8)
Aromatic	50.0 % (43 of 86)	93.0 % (40 of 43)	4.8 % (2 of 42)	100.0 % (1 of 1)
Methyl	100.0 % (94 of 94)	100.0 % (47 of 47)	100.0 % (47 of 47)

1. entity

GDVEKGKKIF IMKCSQCHTV EKGGKHKTGP NLHGLFGRKT GQAPGYSXTA ANKNKGIIWG EDTLMEYLEN PKKYIPGTKM IFVGIKKKEE RADLIAYLKK ATNE

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-99% 15N]		0.7 mM
8	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
9	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
10	phosphate buffer	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
13	entity	natural abundance		0.6 mM
14	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.6 mM
15	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.6 mM
16	phosphate buffer	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2N3Y, Strand ID: A Detail

Release date

2015-06-15

Citation

NMR structure of the Y48pCMF variant of human cytochrome c in its reduced state
Diaz-Moreno, I.
Nat. Struct. Biol.

Related entities 1. Y48pCMF variant of human cytochrome c in its reduced state, entity, : 1 : 15 : 220 entities Detail

Interaction partners 1. Y48pCMF variant of human cytochrome c in its reduced state, entity, : 1 interactors Detail

More details for 1 interactors identified by 1 citations

Experiments performed 15 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 3D 1H-15N NOESY

Instrument

Bruker Avance - 950 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-99% 15N]		0.7 mM
8	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
9	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
10	phosphate buffer	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

3 2D 1H-15N HSQC

Instrument

Bruker Avance - 950 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-99% 15N]		0.7 mM
8	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
9	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
10	phosphate buffer	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

4 2D 1H-13C HSQC

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 2D 1H-1H NOESY

Instrument

Bruker Avance - 950 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
7	entity	[U-99% 15N]		0.7 mM
8	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
9	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
10	phosphate buffer	natural abundance		10 mM
11	H2O	natural abundance		90 %
12	D2O	natural abundance		10 %

6 3D CBCA(CO)NH

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HNCO

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HNCA

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D HN(CO)CA

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 3D HBHA(CO)NH

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

11 3D HCCH-TOCSY

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

12 2D 1H-1H COSY

Instrument

Bruker Avance - 500 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
13	entity	natural abundance		0.6 mM
14	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.6 mM
15	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.6 mM
16	phosphate buffer	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

13 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 500 MHz CITIUS, University of Seville

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
13	entity	natural abundance		0.6 mM
14	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.6 mM
15	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.6 mM
16	phosphate buffer	natural abundance		10 mM
17	H2O	natural abundance		90 %
18	D2O	natural abundance		10 %

14 3D HNCACB

Instrument

Bruker Avance - 700 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

15 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 950 MHz CERM, University of Florence

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.3, Details phosphate buffer 10 mM, pH 6.3

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-99% 13C; U-99% 15N]		0.7 mM
2	P-CARBOXI-METHYL-L-PHENYLALANINE	natural abundance		0.7 mM
3	PROTOPORPHYRIN IX CONTAINING FE	natural abundance		0.7 mM
4	phosphate buffer	natural abundance		10 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25660_2n3y.nef
Input source #2: Coordindates	2n3y.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)
1:47:SER:C	1:48:1PA:N	unknown	unknown	n/a
1:48:1PA:C	1:49:THR:N	unknown	unknown	n/a
1:18:HIS:NE2	2:1:MH0:FE	unknown	unknown	n/a
1:80:MET:SD	2:1:MH0:FE	unknown	unknown	n/a
1:14:CYS:SG	2:1:MH0:CAB	unknown	unknown	n/a
1:17:CYS:SG	2:1:MH0:CAC	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
A	48	1PA	4-(carboxymethyl)-L-phenylalanine	Assigned chemical shifts, Coordinates
B	1	MH0	Mesoheme	None
B	105	HEM	PROTOPORPHYRIN IX CONTAINING FE	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
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSXTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSXTAANKNKGIIWGEDTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKK

----
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_25660_2n3y.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1167		100.0 (chain: A, length: 104), 50.0 (chain: B, length: 2)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	4843 (1)	noe	97.1 (chain: A, length: 104)
2	Distance restraints	DYANA/DIANA_distance_constraints_4	OK	2328 (1)	noe	97.1 (chain: A, length: 104)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	141 (141)	.	96.2 (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: 2, Sequence coverage: 50.0%
- Total number of assignments
  - ¹H chemical shifts: 649
  - ¹³C chemical shifts: 423
  - ¹⁵N chemical shifts: 95
- Completeness of assignments
  - Entity_assemble_ID: A
  - 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

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: 97.1%
- Total number of restraints: 4820
- Weight of restraints: 1.0 (4820)
- Potential type of restraints: upper-bound-parabolic (4820)
- Range of distance target values: 2.6, 6.5 (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
- Saveframe: DYANA/DIANA_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 104, Sequence coverage: 97.1%
  - Total number of restraints: 2318
  - Weight of restraints: 1.0 (2318)
  - Potential type of restraints: upper-bound-parabolic (2318)
  - Range of distance target values: 3.06, 6.5 (Å)
  - Histogram of 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: 96.2%
- Total number of restraints: 141
- Total number of restraints per polymer type: 141
- Weight of restraints: 1.0 (141)
- Potential type of restraints: square-well-parabolic (141)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Apoptosis, Cytochrome c, Electron transfer, Hemeprotein, Mitochondria, Phosphorylation