BMRB Entry 27284

Name: Backbone and side chain resonance assignment of the H-NOX domain from Shewanella woodyi in the Fe(II)CO ligation state
Published: 2018-01-29

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PDB ID: 6ocv
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR27284
MolProbity Validation Chart

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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 and side chain resonance assignment of the H-NOX domain from Shewanella woodyi in the Fe(II)CO ligation state

Deposition date:

2017-10-16

Original release date:

2018-01-29

Authors:

Montfort, William; Chen, Cheng-Yu

Citation:

Citation: Wales, Jessica; Chen, Cheng-Yu; Breci, Linda; Weichsel, Andrzej; Bernier, Sylvie; Sheppeck, James; Solinga, Robert; Nakai, Takashi; Renhowe, Paul; Jung, Joon; Montfort, William. "Discovery of stimulator binding to a conserved pocket in the heme domain of soluble guanylyl cyclase." J. Biol. Chem. 293, 1850-1864 (2018).
PubMed: 29222330

Assembly members:

Assembly members:
SWHNOX, polymer, 190 residues, Formula weight is not available
entity_HEM, non-polymer, 616.487 Da.
entity_CMO, non-polymer, 28.010 Da.

Natural source:

Natural source: Common Name: Shewanella woodyi Taxonomy ID: 60961 Superkingdom: Bacteria Kingdom: not available Genus/species: Shewanella woodyi

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: pET21b+

Entity Sequences (FASTA):

Entity Sequences (FASTA):
SWHNOX: MMGMVFTGLMELIEDEFGYE TLDTLLESCELQSEGIYTSV GSYDHQELLQLVVKLSEVSS VPVTELVRLFGKKLFVELIE GHPEIANEMKDSFDLLSKID SFIHVEVYKLYPQAELPKFT CDRLGDNDIRLHYQSKRPFA SFAEGLLDGCAEYFKEDFTI SRTPETQDSETDVIFNITRA PRGAENLYFQ

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	657
15N chemical shifts	179
1H chemical shifts	1161

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	SWHNOX	1
2	HEME	2
3	CO	3

Entities:

Entity 1, SWHNOX 190 residues - Formula weight is not available

1	MET	MET	GLY	MET	VAL	PHE	THR	GLY	LEU	MET
2	GLU	LEU	ILE	GLU	ASP	GLU	PHE	GLY	TYR	GLU
3	THR	LEU	ASP	THR	LEU	LEU	GLU	SER	CYS	GLU
4	LEU	GLN	SER	GLU	GLY	ILE	TYR	THR	SER	VAL
5	GLY	SER	TYR	ASP	HIS	GLN	GLU	LEU	LEU	GLN
6	LEU	VAL	VAL	LYS	LEU	SER	GLU	VAL	SER	SER
7	VAL	PRO	VAL	THR	GLU	LEU	VAL	ARG	LEU	PHE
8	GLY	LYS	LYS	LEU	PHE	VAL	GLU	LEU	ILE	GLU
9	GLY	HIS	PRO	GLU	ILE	ALA	ASN	GLU	MET	LYS
10	ASP	SER	PHE	ASP	LEU	LEU	SER	LYS	ILE	ASP
11	SER	PHE	ILE	HIS	VAL	GLU	VAL	TYR	LYS	LEU
12	TYR	PRO	GLN	ALA	GLU	LEU	PRO	LYS	PHE	THR
13	CYS	ASP	ARG	LEU	GLY	ASP	ASN	ASP	ILE	ARG
14	LEU	HIS	TYR	GLN	SER	LYS	ARG	PRO	PHE	ALA
15	SER	PHE	ALA	GLU	GLY	LEU	LEU	ASP	GLY	CYS
16	ALA	GLU	TYR	PHE	LYS	GLU	ASP	PHE	THR	ILE
17	SER	ARG	THR	PRO	GLU	THR	GLN	ASP	SER	GLU
18	THR	ASP	VAL	ILE	PHE	ASN	ILE	THR	ARG	ALA
19	PRO	ARG	GLY	ALA	GLU	ASN	LEU	TYR	PHE	GLN

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

1

HEM

Entity 3, CO - C O - 28.010 Da.

1

CMO

Samples:

sample_1: SWHNOX, [U-13C; U-15N], 0.9 ± 0.1 mM

sample_conditions_1: ionic strength: 100 mM; pH: 7.5; pressure: 1 atm; temperature: 293.15 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D HCCH-COSY	sample_1	isotropic	sample_conditions_1

Software:

VNMRJ v4.0, Varian - collection

NMRPipe v8.9, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY v3.131, Goddard - chemical shift assignment, peak picking

NMR spectrometers:

Agilent INOVA 800 MHz

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

1	MET	MET	GLY	MET	VAL	PHE	THR	GLY	LEU	MET
2	GLU	LEU	ILE	GLU	ASP	GLU	PHE	GLY	TYR	GLU
3	THR	LEU	ASP	THR	LEU	LEU	GLU	SER	CYS	GLU
4	LEU	GLN	SER	GLU	GLY	ILE	TYR	THR	SER	VAL
5	GLY	SER	TYR	ASP	HIS	GLN	GLU	LEU	LEU	GLN
6	LEU	VAL	VAL	LYS	LEU	SER	GLU	VAL	SER	SER
7	VAL	PRO	VAL	THR	GLU	LEU	VAL	ARG	LEU	PHE
8	GLY	LYS	LYS	LEU	PHE	VAL	GLU	LEU	ILE	GLU
9	GLY	HIS	PRO	GLU	ILE	ALA	ASN	GLU	MET	LYS
10	ASP	SER	PHE	ASP	LEU	LEU	SER	LYS	ILE	ASP
11	SER	PHE	ILE	HIS	VAL	GLU	VAL	TYR	LYS	LEU
12	TYR	PRO	GLN	ALA	GLU	LEU	PRO	LYS	PHE	THR
13	CYS	ASP	ARG	LEU	GLY	ASP	ASN	ASP	ILE	ARG
14	LEU	HIS	TYR	GLN	SER	LYS	ARG	PRO	PHE	ALA
15	SER	PHE	ALA	GLU	GLY	LEU	LEU	ASP	GLY	CYS
16	ALA	GLU	TYR	PHE	LYS	GLU	ASP	PHE	THR	ILE
17	SER	ARG	THR	PRO	GLU	THR	GLN	ASP	SER	GLU
18	THR	ASP	VAL	ILE	PHE	ASN	ILE	THR	ARG	ALA
19	PRO	ARG	GLY	ALA	GLU	ASN	LEU	TYR	PHE	GLN

1	MET	MET	GLY	MET	VAL	PHE	THR	GLY	LEU	MET
2	GLU	LEU	ILE	GLU	ASP	GLU	PHE	GLY	TYR	GLU
3	THR	LEU	ASP	THR	LEU	LEU	GLU	SER	CYS	GLU
4	LEU	GLN	SER	GLU	GLY	ILE	TYR	THR	SER	VAL
5	GLY	SER	TYR	ASP	HIS	GLN	GLU	LEU	LEU	GLN
6	LEU	VAL	VAL	LYS	LEU	SER	GLU	VAL	SER	SER
7	VAL	PRO	VAL	THR	GLU	LEU	VAL	ARG	LEU	PHE
8	GLY	LYS	LYS	LEU	PHE	VAL	GLU	LEU	ILE	GLU
9	GLY	HIS	PRO	GLU	ILE	ALA	ASN	GLU	MET	LYS
10	ASP	SER	PHE	ASP	LEU	LEU	SER	LYS	ILE	ASP
11	SER	PHE	ILE	HIS	VAL	GLU	VAL	TYR	LYS	LEU
12	TYR	PRO	GLN	ALA	GLU	LEU	PRO	LYS	PHE	THR
13	CYS	ASP	ARG	LEU	GLY	ASP	ASN	ASP	ILE	ARG
14	LEU	HIS	TYR	GLN	SER	LYS	ARG	PRO	PHE	ALA
15	SER	PHE	ALA	GLU	GLY	LEU	LEU	ASP	GLY	CYS
16	ALA	GLU	TYR	PHE	LYS	GLU	ASP	PHE	THR	ILE
17	SER	ARG	THR	PRO	GLU	THR	GLN	ASP	SER	GLU
18	THR	ASP	VAL	ILE	PHE	ASN	ILE	THR	ARG	ALA
19	PRO	ARG	GLY	ALA	GLU	ASN	LEU	TYR	PHE	GLN

1	MET	MET	GLY	MET	VAL	PHE	THR	GLY	LEU	MET
2	GLU	LEU	ILE	GLU	ASP	GLU	PHE	GLY	TYR	GLU
3	THR	LEU	ASP	THR	LEU	LEU	GLU	SER	CYS	GLU
4	LEU	GLN	SER	GLU	GLY	ILE	TYR	THR	SER	VAL
5	GLY	SER	TYR	ASP	HIS	GLN	GLU	LEU	LEU	GLN
6	LEU	VAL	VAL	LYS	LEU	SER	GLU	VAL	SER	SER
7	VAL	PRO	VAL	THR	GLU	LEU	VAL	ARG	LEU	PHE
8	GLY	LYS	LYS	LEU	PHE	VAL	GLU	LEU	ILE	GLU
9	GLY	HIS	PRO	GLU	ILE	ALA	ASN	GLU	MET	LYS
10	ASP	SER	PHE	ASP	LEU	LEU	SER	LYS	ILE	ASP
11	SER	PHE	ILE	HIS	VAL	GLU	VAL	TYR	LYS	LEU
12	TYR	PRO	GLN	ALA	GLU	LEU	PRO	LYS	PHE	THR
13	CYS	ASP	ARG	LEU	GLY	ASP	ASN	ASP	ILE	ARG
14	LEU	HIS	TYR	GLN	SER	LYS	ARG	PRO	PHE	ALA
15	SER	PHE	ALA	GLU	GLY	LEU	LEU	ASP	GLY	CYS
16	ALA	GLU	TYR	PHE	LYS	GLU	ASP	PHE	THR	ILE
17	SER	ARG	THR	PRO	GLU	THR	GLN	ASP	SER	GLU
18	THR	ASP	VAL	ILE	PHE	ASN	ILE	THR	ARG	ALA
19	PRO	ARG	GLY	ALA	GLU	ASN	LEU	TYR	PHE	GLN