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- PDB-2kmy: NMR Solution structures of fully oxidised cytochrome c3 from Desu... -

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Basic information

Entry
Database: PDB / ID: 2kmy
TitleNMR Solution structures of fully oxidised cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774
ComponentsCytochrome c3
KeywordsELECTRON TRANSPORT / Desulfovibrio Desulfuricans / ATCC 27774 / multihaem cytochrome / dipolar shifts / fully oxidised
Function / homology
Function and homology information


electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Class III cytochrome C / Class III cytochrome C family / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c class III / Class III cytochrome C family protein
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsTurner, D.L. / Paixao, V.B. / Vis, H.
CitationJournal: Biochemistry / Year: 2010
Title: Redox linked conformational changes in cytochrome c3 from Desulfovibrio desulfuricans ATCC 27774
Authors: Paixao, V.B. / Vis, H. / Turner, D.L.
History
DepositionAug 5, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 14, 2013Group: Database references
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nmr_software.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0925
Polymers11,6181
Non-polymers2,4744
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c3


Mass: 11618.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Fully oxidized protein sample / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ATCC 27774 / References: UniProt: Q9L915, UniProt: B8J2Z0*PLUS
#2: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Sequence detailsRESIDUE 71 (UNP RESIDUE NUMBER 92) IN DATABASE UNIPROTKB/TREMBL Q9L915 (Q9L915_DESDE) IS LYS IN ...RESIDUE 71 (UNP RESIDUE NUMBER 92) IN DATABASE UNIPROTKB/TREMBL Q9L915 (Q9L915_DESDE) IS LYS IN CURRENT VERSION (32), BUT WAS ARG WHEN FIRST RELEASED ON 2000-10-01.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.8-2.0 mM cytochrome c3-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleUnits: mM / Component: cytochrome c3-1 / Conc. range: 1.8-2.0
Sample conditionsIonic strength: 0,1 / pH: 4.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
XwinNMRBruker Biospindata analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
PARADYANA(INDYANA) Turner et al.structure solution
PARADYANA(INDYANA) Turner et al.refinement
MOLMOLKoradi, Billeter and Wuthrichsuperimposition
MOLMOLKoradi, Billeter and Wuthrichvisual inspection
MOLMOLKoradi, Billeter and Wuthrichrms and mean structure calculations
ProcheckNMRLaskowski and MacArthuridentification and classification of the consensus secondary structure
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 600 / Conformers submitted total number: 20 / Representative conformer: 1

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