BMRB Entry 25389

Name: Backbone 1HN,15N assignments, 15N relaxation data and 3JHNHA coupling constants for wild-type Hydrogenobacter thermophilus cytochrome c552
Published: 2015-08-13

Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR25389

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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

Backbone 1HN,15N assignments, 15N relaxation data and 3JHNHA coupling constants for wild-type Hydrogenobacter thermophilus cytochrome c552

Deposition date:

2014-12-11

Original release date:

2015-08-13

Authors:

Tozawa, Kaeko; Ferguson, Stuart; Redfield, Christina; Smith, Lorna

Citation:

Citation: Tozawa, Kaeko; Ferguson, Stuart; Redfield, Christina; Smith, Lorna. "Comparison of the backbone dynamics of wild-type Hydrogenobacter thermophilus cytochrome c(552) and its b-type variant" J. Biomol. NMR 62, 221-231 (2015).
PubMed: 25953310

Assembly members:

Assembly members:
wt_cytc, polymer, 80 residues, Formula weight is not available
entity_HEM, non-polymer, 616.487 Da.

Natural source:

Natural source: Common Name: aquificales Taxonomy ID: 940 Superkingdom: Bacteria Kingdom: not available Genus/species: Hydrogenobacter thermophilus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: not known

Entity Sequences (FASTA):

Entity Sequences (FASTA):
wt_cytc: NEQLAKQKGCMACHDLKAKK VGPAYADVAKKYAGRKDAVD YLAGKIKKGGSGVWGSVPMP PQNVTDAEAKQLAQWILSIK

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1
coupling_constants
- coupling_constant_list_1
heteronucl_NOEs
- heteronuclear_noe_list_1
heteronucl_T1_relaxation
- heteronuclear_T1_list_1
heteronucl_T2_relaxation
- heteronuclear_T2_list_1

Data type	Count
15N chemical shifts	75
1H chemical shifts	75
T1 relaxation values	71
T2 relaxation values	71
coupling constants	64
heteronuclear NOE values	71

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	wt_cytc	1
2	heme	2

Entities:

Entity 1, wt_cytc 80 residues - Formula weight is not available

1	ASN	GLU	GLN	LEU	ALA	LYS	GLN	LYS	GLY	CYS
2	MET	ALA	CYS	HIS	ASP	LEU	LYS	ALA	LYS	LYS
3	VAL	GLY	PRO	ALA	TYR	ALA	ASP	VAL	ALA	LYS
4	LYS	TYR	ALA	GLY	ARG	LYS	ASP	ALA	VAL	ASP
5	TYR	LEU	ALA	GLY	LYS	ILE	LYS	LYS	GLY	GLY
6	SER	GLY	VAL	TRP	GLY	SER	VAL	PRO	MET	PRO
7	PRO	GLN	ASN	VAL	THR	ASP	ALA	GLU	ALA	LYS
8	GLN	LEU	ALA	GLN	TRP	ILE	LEU	SER	ILE	LYS

Entity 2, heme - C34 H32 Fe N4 O4 - 616.487 Da.

1

HEM

Samples:

sample_1: wt_cytc, [U-98% 15N], 0.7 mM; sodium phosphate 20 mM

sample_conditions_1: ionic strength: 0.08 M; pH: 7.1; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
15N T1 experiments	sample_1	isotropic	sample_conditions_1
15N T2 experiments	sample_1	isotropic	sample_conditions_1
15N heteronuclear NOE experiment	sample_1	isotropic	sample_conditions_1
2D 1H-15N HMQCJ	sample_1	isotropic	sample_conditions_1

Software:

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

CCPN_Analysis, CCPN - chemical shift assignment, data analysis

NMR spectrometers:

Home-built OMEGA 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

1	ASN	GLU	GLN	LEU	ALA	LYS	GLN	LYS	GLY	CYS
2	MET	ALA	CYS	HIS	ASP	LEU	LYS	ALA	LYS	LYS
3	VAL	GLY	PRO	ALA	TYR	ALA	ASP	VAL	ALA	LYS
4	LYS	TYR	ALA	GLY	ARG	LYS	ASP	ALA	VAL	ASP
5	TYR	LEU	ALA	GLY	LYS	ILE	LYS	LYS	GLY	GLY
6	SER	GLY	VAL	TRP	GLY	SER	VAL	PRO	MET	PRO
7	PRO	GLN	ASN	VAL	THR	ASP	ALA	GLU	ALA	LYS
8	GLN	LEU	ALA	GLN	TRP	ILE	LEU	SER	ILE	LYS

1	ASN	GLU	GLN	LEU	ALA	LYS	GLN	LYS	GLY	CYS
2	MET	ALA	CYS	HIS	ASP	LEU	LYS	ALA	LYS	LYS
3	VAL	GLY	PRO	ALA	TYR	ALA	ASP	VAL	ALA	LYS
4	LYS	TYR	ALA	GLY	ARG	LYS	ASP	ALA	VAL	ASP
5	TYR	LEU	ALA	GLY	LYS	ILE	LYS	LYS	GLY	GLY
6	SER	GLY	VAL	TRP	GLY	SER	VAL	PRO	MET	PRO
7	PRO	GLN	ASN	VAL	THR	ASP	ALA	GLU	ALA	LYS
8	GLN	LEU	ALA	GLN	TRP	ILE	LEU	SER	ILE	LYS

1	ASN	GLU	GLN	LEU	ALA	LYS	GLN	LYS	GLY	CYS
2	MET	ALA	CYS	HIS	ASP	LEU	LYS	ALA	LYS	LYS
3	VAL	GLY	PRO	ALA	TYR	ALA	ASP	VAL	ALA	LYS
4	LYS	TYR	ALA	GLY	ARG	LYS	ASP	ALA	VAL	ASP
5	TYR	LEU	ALA	GLY	LYS	ILE	LYS	LYS	GLY	GLY
6	SER	GLY	VAL	TRP	GLY	SER	VAL	PRO	MET	PRO
7	PRO	GLN	ASN	VAL	THR	ASP	ALA	GLU	ALA	LYS
8	GLN	LEU	ALA	GLN	TRP	ILE	LEU	SER	ILE	LYS