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

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Basic information

Entry
Database: PDB / ID: 1ehj
TitleA PROTON-NMR INVESTIGATION OF THE FULLY REDUCED CYTOCHROME C7 FROM DESULFUROMONAS ACETOXIDANS
ComponentsCYTOCHROME C7
KeywordsELECTRON TRANSPORT / multi-heme
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
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, torsion angle dynamics restrained energy minimization
AuthorsAssfalg, M. / Banci, L. / Bertini, I. / Bruschi, M. / Giudici-Orticoni, M.T.
Citation
Journal: 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.
#1: Journal: Eur.J.Biochem. / Year: 1998
Title: 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans.
Authors: Assfalg, M. / Banci, L. / Bertini, I. / Bruschi, M. / Turano, P.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans.
Authors: Banci, L. / Bertini, I. / Bruschi, M. / Sompornpisut, P. / Turano, P.
History
DepositionFeb 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 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_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 1.4Nov 6, 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)1 / -
Representative

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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
111TOCSY
221TOCSY
331TOCSY
2412D NOESY
3512D NOESY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 2-3mM cytochrome 1H; 100mM phosphate buffer / Solvent system: 90% H2O/10% D2O
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
15.5ambient 292 K
26.5ambient 292 K
38ambient 292 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AMXBrukerAMX5002

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Processing

NMR software
NameVersionClassification
Amber4.1refinement
DYANA1.5structure solution
XEASY3.1data analysis
XwinNMRprocessing
RefinementMethod: simulated annealing, torsion angle dynamics restrained energy minimization
Software ordinal: 1
Details: The structures are based on a total of 1352 NOE-derived constraints
NMR ensembleConformers submitted total number: 1

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