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- PDB-1i6e: SOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRI... -

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Basic information

Entry
Database: PDB / ID: 1i6e
TitleSOLUTION STRUCTURE OF THE FUNCTIONAL DOMAIN OF PARACOCCUS DENITRIFICANS CYTOCHROME C552 IN THE OXIDIZED STATE
ComponentsCYTOCHROME C552
KeywordsELECTRON TRANSPORT / CYTOCHROME C552 / HEME / REDOX STATES / ISOTOPE ENRICHMENT {13C/15N} / NMR SPECTROSCOPY / SOLUTION STRUCTURE
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c, class IA/ IB / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodSOLUTION NMR / DISTANCE GEOMETRY, ENERGY MINIMIZATION
AuthorsReincke, B. / Perez, C. / Pristovsek, P. / Luecke, C. / Ludwig, C. / Loehr, F. / Rogov, V.V. / Ludwig, B. / Rueterjans, H.
Citation
Journal: Biochemistry / Year: 2001
Title: Solution structure and dynamics of the functional domain of Paracoccus denitrificans cytochrome c(552) in both redox states.
Authors: Reincke, B. / Perez, C. / Pristovsek, P. / Lucke, C. / Ludwig, C. / Lohr, F. / Rogov, V.V. / Ludwig, B. / Ruterjans, H.
#1: Journal: Eur.J.Biochem. / Year: 2000
Title: Solution Structure of the Functional Domain of Paracoccus Denitrificans Cytochrome C552 in the Reduced State
Authors: Pristovsek, P. / Luecke, C. / Reincke, B. / Ludwig, B. / Rueterjans, H.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: Structure of the Soluble Domain of Cytochrome C552 from Paracoccus Denitrificans in the Oxidized and Reduced States
Authors: Harrenga, A. / Reincke, B. / Rueterjans, H. / Ludwig, B. / Michel, H.
#3: Journal: Biochim.Biophys.Acta / Year: 1999
Title: Heterologous Expression of Soluble Fragments of Cytochrome C552 Acting as Electron Donor to the Paracoccus Denitrificans Cytochrome C Oxidase
Authors: Reincke, B. / Thoeny-Meyer, L. / Dannehl, C. / Odenwald, A. / Aidim, M. / Witt, H. / Rueterjans, H. / Ludwig, B.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / 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 / _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_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 C552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1722
Polymers10,5541
Non-polymers6191
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LEAST RESTRAINT VIOLATIONS
Representative

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Components

#1: Protein CYTOCHROME C552


Mass: 10553.977 Da / Num. of mol.: 1 / Fragment: SOLUBLE FUNCTIONAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: COVALENT THIOETHER LINKAGES FROM HEME COFACTOR TO BOTH CYS14 AND CYS17
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Strain: PD1235 / Description: HETEROLOGOUS EXPRESSION / Cellular location: PERIPLASM / Gene: CYCM / Plasmid: PET22B+ / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P54820
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / 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
1111H-1H TOCSY
1211H-1H NOESY
1311H-15N HSQC
1411H-15N TOCSY-HSQC
1511H-15N NOESY-HSQC
161HN(CA)CB
171CC(CO)NH-TOCSY
181(H)CCH-TOCSY
191(HCA)CO(CA)NH
11011H-13C HSQC
11111H-13C NOESY-HSQC
11211D NOE DIFFERENCE SPECTRA
NMR detailsText: THE EXPERIMENTS WERE PERFORMED WITH OXIDIZED UNLABELED, 15N-LABELED OR 13C-LABELED CYTOCHROME C552.

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Sample preparation

DetailsContents: 20 MM PHOSPHATE, 90% H2O/ 10% D2O
Sample conditionspH: 5.5 / Temperature: 298.00 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Discover97MSIrefinement
DYANA1.5structure solution
Discover97structure solution
RefinementMethod: DISTANCE GEOMETRY, ENERGY MINIMIZATION / Software ordinal: 1 / Details: ENERGY MINIMIZATION.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20

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