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- PDB-7o9u: Solution structure of oxidized cytochrome c552 from Thioalkalivib... -

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Basic information

Entry
Database: PDB / ID: 7o9u
TitleSolution structure of oxidized cytochrome c552 from Thioalkalivibrio paradoxus
ComponentsCytochrome c552
KeywordsELECTRON TRANSPORT / thiocyanate dehydrogenase electron acceptor / cytochrome c552 / class I cytochrome c / hemeprotein / periplasmic
Function / homologyHEME C
Function and homology information
Biological speciesThioalkalivibrio paradoxus ARh 1 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsBritikov, V.V. / Britikova, E.V. / Altukhov, D.A. / Timofeev, V.I. / Dergousova, N.I. / Rakitina, T.V. / Tikhonova, T.V. / Usanov, S.A. / Popov, V.O. / Bocharov, E.V.
Funding support Russian Federation, 2items
OrganizationGrant numberCountry
Russian Science Foundation20-14-00314 Russian Federation
Russian Foundation for Basic Research20-54-00041 Russian Federation
CitationJournal: Int J Mol Sci / Year: 2022
Title: Unusual Cytochrome c 552 from Thioalkalivibrio paradoxus : Solution NMR Structure and Interaction with Thiocyanate Dehydrogenase.
Authors: Britikov, V.V. / Bocharov, E.V. / Britikova, E.V. / Dergousova, N.I. / Kulikova, O.G. / Solovieva, A.Y. / Shipkov, N.S. / Varfolomeeva, L.A. / Tikhonova, T.V. / Timofeev, V.I. / Shtykova, E. ...Authors: Britikov, V.V. / Bocharov, E.V. / Britikova, E.V. / Dergousova, N.I. / Kulikova, O.G. / Solovieva, A.Y. / Shipkov, N.S. / Varfolomeeva, L.A. / Tikhonova, T.V. / Timofeev, V.I. / Shtykova, E.V. / Altukhov, D.A. / Usanov, S.A. / Arseniev, A.S. / Rakitina, T.V. / Popov, V.O.
History
DepositionApr 17, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionMay 5, 2021ID: 6TK0
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3562
Polymers16,7371
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1120 Å2
ΔGint-20 kcal/mol
Surface area11390 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c552


Mass: 16737.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thioalkalivibrio paradoxus ARh 1 (bacteria)
Gene: WP_006748979.1 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D 1H-15N NOESY
1161isotropic23D 1H-15N NOESY
151isotropic13D 1H-15N TOCSY
161isotropic13D 1H-13C NOESY aliphatic
171isotropic13D HNCA
181isotropic13D HN(CO)CA
191isotropic13D HNCO
1101isotropic13D HCACO
1111isotropic13D HNHA
1121isotropic13D (H)CCH-TOCSY
1131isotropic13D HN(CA)CB
1141isotropic13D HBHA(CO)NH
1151isotropic13D H(CCO)NH
1172isotropic12D 1H-1H NOESY
1182isotropic12D 1H-1H TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.6 mM [U-100% 13C; U-100% 15N] Cytochrome c552, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
solution20.6 mM Cytochrome c552, 95% H2O/5% D2Ounlabeled_sample95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCytochrome c552[U-100% 13C; U-100% 15N]1
0.6 mMCytochrome c552natural abundance2
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 7.0 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
TopSpin3.2Bruker Biospinprocessing
CcpNmr AnalysisCCPNdata analysis
CcpNmr AnalysisCCPNpeak picking
ARIA2.3Linge, O'Donoghue and Nilgeschemical shift assignment
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
X-PLOR NIH3.2Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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