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- PDB-5mcs: Solution structure and dynamics of the outer membrane cytochrome ... -

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Basic information

Entry
Database: PDB / ID: 5mcs
TitleSolution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens
ComponentsLipoprotein cytochrome c, 1 heme-binding site
KeywordsELECTRON TRANSPORT / Geobacter sulfurreducens / outer membrane cytochrome / redox protein / solution structure
Function / homology
Function and homology information


plasma membrane-derived thylakoid lumen / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Lipoprotein cytochrome c, 1 heme-binding site
Similarity search - Component
Biological speciesGeobacter sulfurreducens (bacteria)
MethodSOLUTION NMR / distance geometry
AuthorsDantas, J.M. / Silva, M.A. / Morgado, L. / Pantoja-Uceda, D. / Turner, D.L. / Bruix, M. / Salgueiro, C.A.
Funding support Portugal, 2items
OrganizationGrant numberCountry
Fundacao FCTPTDC/BBB-BQB/3554/2014 Portugal
Fundacao FCTUID/Multi/04378/2013 Portugal
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Solution structure and dynamics of the outer membrane cytochrome OmcF from Geobacter sulfurreducens.
Authors: Dantas, J.M. / Silva, M.A. / Pantoja-Uceda, D. / Turner, D.L. / Bruix, M. / Salgueiro, C.A.
History
DepositionNov 10, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_seq_map_depositor_info
Item: _pdbx_nmr_software.name / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipoprotein cytochrome c, 1 heme-binding site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9432
Polymers8,3241
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1160 Å2
ΔGint-22 kcal/mol
Surface area5140 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #20target function

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Components

#1: Protein Lipoprotein cytochrome c, 1 heme-binding site / Outer membrane protein / OmcF


Mass: 8324.456 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (strain ATCC 51573 / DSM 12127 / PCA) (bacteria)
Gene: omcF, GSU2432 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: Q74AE4
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D CBCA(CO)NH
121isotropic23D HNCA
131isotropic23D HN(CA)CB
141isotropic23D HN(CO)CA
151isotropic23D (H)CCH-TOCSY
1111isotropic22D 1H-15N HSQC
2102isotropic22D 1H-1H COSY
292isotropic22D 1H-1H TOCSY
282isotropic22D 1H-1H NOESY
373isotropic12D 1H-1H COSY
363isotropic12D 1H-1H TOCSY
3123isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM [U-13C; U-15N] Outer membrane protein, OmcF, 90% H2O/10% D2O15N_13C_OmcF90% H2O/10% D2O
solution22 mM Outer membrane protein, OmcF, 90% H2O/10% D2O1H_OmcF90% H2O/10% D2O
solution32 mM Outer membrane protein, OmcF, 100% D2O1H_OmcF100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMOuter membrane protein, OmcF[U-13C; U-15N]1
2 mMOuter membrane protein, OmcFnatural abundance2
2 mMOuter membrane protein, OmcFnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1100 mM15N_13C7 1 atm298 K
2100 mM1H7 1 atm298 K
3100 mM1H_D2O7 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
DYANAGuntert P.refinement
DYANAGuntert, Braun and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
RefinementMethod: distance geometry / Software ordinal: 1
NMR representativeSelection criteria: target function
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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