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- PDB-1new: Cytochrome C551.5, NMR -

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Basic information

Entry
Database: PDB / ID: 1new
TitleCytochrome C551.5, NMR
ComponentsCYTOCHROME C551.5
KeywordsELECTRON TRANSPORT / CYTOCHROME / MULTIHEME CYTOCHROME / CYTOCHROME C7
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 / TORSION ANGLE MOLECULAR DYNAMICS
AuthorsAssfalg, M. / Banci, L. / Bertini, I. / Bruschi, M. / Turano, P.
Citation
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.
#1: 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.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1996
Title: Structure of the Three-Haem Core of Cytochrome C551.5 Determined by 1H NMR
Authors: Coutinho, I.B. / Turner, D.L. / Liu, M.Y. / Legall, J. / Xavier, A.V.
#3: Journal: Eur.J.Biochem. / Year: 1984
Title: Nuclear-Magnetic-Resonance Studies of Desulfuromonas Acetoxidans Cytochrome C551.5 (C7)
Authors: Moura, J.G. / Moore, G.R. / Williams, R.J. / Probst, I. / Legall, J. / Xavier, A.V.
#4: Journal: FEBS Lett. / Year: 1971
Title: The Amino Acid Resequence of Cytochrome C-551.5 (Cytochrome C7) from the Green Photosynthetic Bacterium Chloropseudomonas Ethylica
Authors: Ambler, R.P.
History
DepositionFeb 10, 1998Processing site: BNL
SupersessionApr 29, 1998ID: 1CFO
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
SupersessionJan 26, 2010ID: 2NEW
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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 C551.5
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 / 1000MINIMUM TARGET FUNCTION VALUE
Representative

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Components

#1: Protein CYTOCHROME C551.5 / CYTOCHROME C7 / TRIHEME CYTOCHROME


Mass: 7280.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CLASS III OF C-TYPE CYTOCHROMES, FULLY OXIDIZED FORM
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 experimentType: NOESY

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DMX800 / Manufacturer: Bruker / Model: DMX800 / Field strength: 800 MHz

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameDeveloperClassification
DYANAGUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: TORSION ANGLE MOLECULAR DYNAMICS / Software ordinal: 1 / Details: ENERGY MINIMIZATION BY THE SANDER MODULE OF AMBER
NMR ensembleConformer selection criteria: MINIMUM TARGET FUNCTION VALUE / Conformers calculated total number: 1000 / Conformers submitted total number: 35

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