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- PDB-1f22: A PROTON-NMR INVESTIGATION OF THE FULLY REDUCED CYTOCHROME C7 FRO... -

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Basic information

Entry
Database: PDB / ID: 1f22
TitleA PROTON-NMR INVESTIGATION OF THE FULLY REDUCED CYTOCHROME C7 FROM DESULFUROMONAS ACETOXIDANS. COMPARISON BETWEEN THE REDUCED AND THE OXIDIZED FORMS.
ComponentsCYTOCHROME C7
KeywordsELECTRON TRANSPORT / triheme
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c7 and related cytochrome c / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDesulfuromonas acetoxidans (bacteria)
MethodSOLUTION NMR / simulated annealing, energy minimization
AuthorsAssfalg, M. / Banci, L. / Bertini, I. / Bruschi, M. / Giudici-Orticoni, M.T.
CitationJournal: Eur.J.Biochem. / Year: 1999
Title: A proton-NMR investigation of the fully reduced cytochrome c7 from Desulfuromonas acetoxidans. Comparison between the reduced and the oxidized forms.
Authors: Assfalg, M. / Banci, L. / Bertini, I. / Bruschi, M. / Giudici-Orticoni, M.T.
History
DepositionMay 23, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1364
Polymers7,2801
Non-polymers1,8563
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 35all calculated structures submitted
RepresentativeModel #1fewest violations

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Components

#1: Protein CYTOCHROME C7


Mass: 7280.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfuromonas acetoxidans (bacteria) / References: UniProt: P00137
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2-3mM cytochrome c7; 10mM phosphate buffer; catalytic amounts of D. vulgaris hydrogenase
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 0.1 mM / pH: 6.5 / Pressure: ambient / Temperature: 292 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR softwareName: DYANA / Version: 1.5 / Developer: Wuthrich / Classification: refinement
RefinementMethod: simulated annealing, energy minimization / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 35 / Conformers submitted total number: 35

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