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- PDB-2fwl: The cytochrome c552/CuA complex from Thermus thermophilus -

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Basic information

Entry
Database: PDB / ID: 2fwl
TitleThe cytochrome c552/CuA complex from Thermus thermophilus
Components
  • Cytochrome c oxidase subunit II
  • Cytochrome c-552
KeywordsELECTRON TRANSPORT/OXIDOREDUCTASE / docking calculations / redox protein complex / electron transfer pathway / ELECTRON TRANSPORT-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase activity / : / electron transfer activity / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Ba3-like heme-copper oxidase subunit II, C-terminal / : / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c / Cytochrome c-like domain ...Ba3-like heme-copper oxidase subunit II, C-terminal / : / : / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DINUCLEAR COPPER ION / HEME C / Cytochrome c-552 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodSOLUTION NMR / docking calculations
AuthorsMuresanu, L. / Pristovsek, P. / Loehr, F. / Maneg, O. / Mukrasch, M.D. / Rueterjans, H. / Ludwig, B. / Luecke, C.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The electron transfer complex between cytochrome c552 and the CuA domain of the Thermus thermophilus ba3 oxidase - a combined NMR and computational approach
Authors: Muresanu, L. / Pristovsek, P. / Loehr, F. / Maneg, O. / Mukrasch, M.D. / Rueterjans, H. / Ludwig, B. / Luecke, C.
History
DepositionFeb 2, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c-552
B: Cytochrome c oxidase subunit II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0904
Polymers29,3452
Non-polymers7462
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)3 / 10structures with the lowest energy
RepresentativeModel #1fewest violations

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Components

#1: Protein Cytochrome c-552 / Cytochrome c552


Mass: 14396.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04164
#2: Protein Cytochrome c oxidase subunit II / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase polypeptide II / ba3 oxidase subunit II / CuA domain


Mass: 14947.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-3d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P98052, cytochrome-c oxidase
#3: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 15N separated TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM cytochrome c552 U-15N, 20mM phosphate buffer, 2mM CuA domain, 95% H2O, 5% D2O95% H2O/5% D2O
20.5mM CuA domain U-15N, 20mM phosphate buffer, 2mM cytochrome c552, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditionsIonic strength: 20mM phosphate buffer / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK1.3Bonvinstructure solution
HADDOCK1.3Bonvinrefinement
RefinementMethod: docking calculations / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 3

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