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- PDB-2k3v: Solution Structure of a Tetrahaem Cytochrome from Shewanella Frig... -

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Basic information

Entry
Database: PDB / ID: 2k3v
TitleSolution Structure of a Tetrahaem Cytochrome from Shewanella Frigidimarina
ComponentsTetraheme cytochrome c-type
KeywordsELECTRON TRANSPORT / Multihaem cytochromes / Redox proteins / Shewanella / Heme / Iron / Metal-binding / Periplasm / Transport
Function / homology
Function and homology information


: / periplasmic space / metal ion binding
Similarity search - Function
Tetrahaem cytochrome domain / Cytochrome c3 / : / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Tetraheme cytochrome c-type
Similarity search - Component
Biological speciesShewanella frigidimarina (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsPaixao, V.B. / Turner, D.L. / Salgueiro, C.A. / Brennan, L. / Reid, G.A. / Chapman, S.K.
CitationJournal: Biochemistry / Year: 2008
Title: The solution structure of a tetraheme cytochrome from Shewanella frigidimarina reveals a novel family structural motif
Authors: Paixao, V.B. / Salgueiro, C.A. / Brennan, L. / Reid, G.A. / Chapman, S.K. / Turner, D.L.
History
DepositionMay 19, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Oct 2, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_sample_details.contents / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tetraheme cytochrome c-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8045
Polymers9,3301
Non-polymers2,4744
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4060 Å2
ΔGint-72 kcal/mol
Surface area5910 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 600target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Tetraheme cytochrome c-type / Cytochrome c3 / Sfc


Mass: 9330.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella frigidimarina (bacteria) / Strain: NCIMB 400 / Gene: cctA, Sfri_1504 / Production host: Escherichia coli (E. coli) / References: UniProt: O33731
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1312D DQF-COSY
1422D 1H-1H NOESY
1522D 1H-1H TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
13 mM Sfc, 92% H2O/8% D2O92% H2O/8% D2O
23 mM Sfc, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
3 mMSfc1
3 mMSfc2
Sample conditionsIonic strength: 0.1 / pH: 6.1 / Pressure: ambient atm / Temperature: 303 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
NameVersionDeveloperClassification
XWIN-NMRBruker Biospindata analysis
XEASYBartels et al.peak picking
SparkyGoddardintegration
SparkyGoddardpeak picking
PARADYANA(INDYANA) Turner et al.structure solution
MOLMOL2Koradi, Billeter and Wuthrichsuperimposition
MOLMOL2Koradi, Billeter and Wuthrichvisual inspection
MOLMOL2Koradi, Billeter and Wuthrichrms and mean structure calculations
WHAT IF20030529-0952Vriendstereochemical analysis
ProcheckNMRLaskowski and MacArthuridentification and classification of the consensus secondary structure
PARADYANA(INDYANA) Turner et al.refinement
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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