BMRB Entry 34618

Name: Solution structure of oxidized cytochrome c552 from Thioalkalivibrio paradoxus
Published: 2021-05-03

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PDB ID: 7o9u
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34618
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:

Solution structure of oxidized cytochrome c552 from Thioalkalivibrio paradoxus

Deposition date:

2021-04-17

Original release date:

2021-05-03

Authors:

Britikov, V.; Britikova, E.; Altukhov, D.; Timofeev, V.; Dergousova, N.; Rakitina, T.; Tikhonova, T.; Usanov, S.; Popov, V.; Bocharov, E.

Citation:

Citation: Britikov, Vladimir; Bocharov, Eduard; Britikova, Elena; Dergousova, Natalia; Kulikova, Olga; Solovieva, Anastasia; Shipkov, Nikolai; Varfolomeeva, Larisa; Tikhonova, Tamara; Timofeev, Vladimir; Shtykova, Eleonora; Altukhov, Dmitry; Usanov, Sergey; Arseniev, Alexander; Rakitina, Tatiana; Popov, Vladimir. "Unusual Cytochrome c 552 from Thioalkalivibrio paradoxus: Solution NMR Structure and Interaction with Thiocyanate Dehydrogenase" Int. J. Mol. Sci. 23, 9969-9969 (2022).
PubMed: 36077365

Assembly members:

Assembly members:
entity_1, polymer, 153 residues, 16737.066 Da.
entity_HEC, non-polymer, 618.503 Da.

Natural source:

Natural source: Common Name: Thioalkalivibrio paradoxus ARh 1 Taxonomy ID: 713585 Superkingdom: Bacteria Kingdom: not available Genus/species: Thioalkalivibrio paradoxus

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3)

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MDIGINSDPHPPHHHDHHGH GSGWEVPEAEIHRENPIPPD ARSLDQGGVLYAEHCVRCHG ETLRGDGPDAHDLDPPVADL VEHAPHHSDGDLAYRVRIGR GPMPGFGDALDERDIWDLVN FMRDRAQGAALAGTNGHSPD HAAGDHHHGDHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1

Data type	Count
13C chemical shifts	451
15N chemical shifts	121
1H chemical shifts	740

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 153 residues - 16737.066 Da.

1

MET

ASP

ILE

GLY

ILE

ASN

SER

ASP

PRO

HIS

2

PRO

HIS

ASP

HIS

GLY

HIS

3

GLY

SER

GLY

TRP

GLU

VAL

PRO

GLU

ALA

GLU

4

ILE

HIS

ARG

GLU

ASN

PRO

ILE

PRO

ASP

5

ALA

ARG

SER

LEU

ASP

GLN

GLY

VAL

LEU

6

TYR

ALA

GLU

HIS

CYS

VAL

ARG

CYS

HIS

GLY

7

GLU

THR

LEU

ARG

GLY

ASP

GLY

PRO

ASP

ALA

8

HIS

ASP

LEU

ASP

PRO

VAL

ALA

ASP

LEU

9

VAL

GLU

HIS

ALA

PRO

HIS

SER

ASP

GLY

10

ASP

LEU

ALA

TYR

ARG

VAL

ARG

ILE

GLY

ARG

11

GLY

PRO

MET

PRO

GLY

PHE

GLY

ASP

ALA

LEU

12

ASP

GLU

ARG

ASP

ILE

TRP

ASP

LEU

VAL

ASN

13

PHE

MET

ARG

ASP

ARG

ALA

GLN

GLY

ALA

14

LEU

ALA

GLY

THR

ASN

GLY

HIS

SER

PRO

ASP

15

HIS

ALA

GLY

ASP

HIS

GLY

ASP

16

HIS

Entity 2, unit_2 - C34 H34 Fe N4 O4 - 618.503 Da.

1

HEC

Samples:

sample_1: Cytochrome c552, [U-100% 13C; U-100% 15N], 0.6 mM; potassium phosphate buffer 50 mM

sample_2: Cytochrome c552 0.6 mM; potassium phosphate buffer 50 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 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 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-15N TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HCACO	sample_1	isotropic	sample_conditions_1
3D HNHA	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	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 H(CCO)NH	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

TopSpin v3.2, Bruker Biospin - collection, processing

CcpNmr Analysis, CCPN - data analysis, peak picking

ARIA v2.3, Linge, O'Donoghue and Nilges - chemical shift assignment

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

X-PLOR NIH v3.2, Schwieters, Kuszewski, Tjandra and Clore - refinement

NMR spectrometers:

Bruker AVANCE III 600 MHz
Bruker AVANCE III 800 MHz

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