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PDB ID: 9vr0
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36771
MolProbity Validation Chart

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NMR-STAR v3 text file.
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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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Name: NMR solution structure of termini-truncated oxidized cytochrome c552 from Thioalkalivibrio paradoxus
Published: 2026-02-06

Title:

NMR solution structure of termini-truncated oxidized cytochrome c552 from Thioalkalivibrio paradoxus

Deposition date:

2025-07-05

Original release date:

2026-02-06

Authors:

Britikov, V.; Britikova, E.; Rakitina, T.; Dergousova, N.; Tikhonova, T.; Popov, V.; Bocharov, E.

Citation:

Citation: Britikov, V.; Britikova, E.; Rakitina, T.; Dergousova, N.; Tikhonova, T.; Popov, V.; Bocharov, E.. "NMR solution structure of termini-truncated oxidized cytochrome c552 from Thioalkalivibrio paradoxus" .

Assembly members:

Assembly members:
Cytochrome c552, polymer, 125 residues, 13772.092 Da.
HEME C, non-polymer, 618.503 Da.

Natural source:

Natural source: Common Name: Thioalkalivibrio paradoxus ARh 1 Taxonomy ID: 713585 Superkingdom: Bacteria Kingdom: Pseudomonadati Genus/species: Thioalkalivibrio paradoxus

Experimental source:

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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
Cytochrome c552: MGSGWEVPEAEIHRENPIPP DARSLDQGGVLYAEHCVRCH GETLRGDGPDAHDLDPPVAD LVEHAPHHSDGDLAYRVRIG RGPMPGFGDALDERDIWDLV NFMRDRAQGAALAGTNGLEH HHHHH

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	407
15N chemical shifts	109
1H chemical shifts	668

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_HEC	2

Entities:

Entity 1, entity_1 125 residues - 13772.092 Da.

1

MET

GLY

SER

GLY

TRP

GLU

VAL

PRO

GLU

ALA

2

GLU

ILE

HIS

ARG

GLU

ASN

PRO

ILE

PRO

3

ASP

ALA

ARG

SER

LEU

ASP

GLN

GLY

VAL

4

LEU

TYR

ALA

GLU

HIS

CYS

VAL

ARG

CYS

HIS

5

GLY

GLU

THR

LEU

ARG

GLY

ASP

GLY

PRO

ASP

6

ALA

HIS

ASP

LEU

ASP

PRO

VAL

ALA

ASP

7

LEU

VAL

GLU

HIS

ALA

PRO

HIS

SER

ASP

8

GLY

ASP

LEU

ALA

TYR

ARG

VAL

ARG

ILE

GLY

9

ARG

GLY

PRO

MET

PRO

GLY

PHE

GLY

ASP

ALA

10

LEU

ASP

GLU

ARG

ASP

ILE

TRP

ASP

LEU

VAL

11

ASN

PHE

MET

ARG

ASP

ARG

ALA

GLN

GLY

ALA

12

ALA

LEU

ALA

GLY

THR

ASN

GLY

LEU

GLU

HIS

13

HIS

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

1

HEC

Samples:

sample_1: Cytochrome c552, [U-100% 13C; U-100% 15N], 0.6 mM; sodium phosphate buffer 50 mM; H2O 95%; D2O, [U-2H], 5%

sample_2: Cytochrome c552 0.6 mM; sodium phosphate buffer 50 mM; H2O 95%; D2O, [U-2H], 5%

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
2D 1H-1H NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-1H TOCSY	sample_2	isotropic	sample_conditions_1

Software:

CcpNmr Analysis v2.5.2, CCPN - chemical shift assignment

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement

CNS v1.3, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

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

CcpNmr Analysis v2.5.2, CCPN - peak picking

TopSpin v3.2, Bruker Biospin - collection

TopSpin v3.2, Bruker Biospin - processing

NMR spectrometers:

Bruker AVANCE III 600 MHz

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

BMRB Entry 36771