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- PDB-1kx2: Minimized average structure of a mono-heme ferrocytochrome c from... -

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Basic information

Entry
Database: PDB / ID: 1kx2
TitleMinimized average structure of a mono-heme ferrocytochrome c from Shewanella putrefaciens
Componentsmono-heme c-type cytochrome ScyA
KeywordsOXYGEN STORAGE/TRANSPORT / haem protein / ferrocytochrome / electron transport / gram negative / bacteria / ScyA Shewanella Putrefaciens / mono haem / all-alpha / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class IE / Cytochrome C oxidase, cbb3-type, subunit III / 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 / Mono-heme c-type cytochrome ScyA
Similarity search - Component
Biological speciesShewanella putrefaciens (bacteria)
MethodSOLUTION NMR / simulated annealing in the dihedral angle space in DYANA in 15000 steps; 30 structures with the lowest target function out of a total number of 250 generated structures constitute the REM family - subject to restrained energy minimization in AMBER; the minimized mean is reported
Model type detailsminimized average
AuthorsBartalesi, I. / Bertini, I. / Hajieva, P. / Rosato, A. / Vasos, P.R.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure of a monoheme ferrocytochrome c from Shewanella putrefaciens and structural analysis of sequence-similar proteins: functional implications.
Authors: Bartalesi, I. / Bertini, I. / Hajieva, P. / Rosato, A. / Vasos, P.R.
History
DepositionJan 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2002Provider: 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / 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_software.name / _pdbx_nmr_spectrometer.model / _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
Remark 999SEQUENCE Recombinant protein, without the signaling peptide. The first three amino-acids (Ala Asp ...SEQUENCE Recombinant protein, without the signaling peptide. The first three amino-acids (Ala Asp Leu) have been added for protein expression purposes.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: mono-heme c-type cytochrome ScyA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2192
Polymers8,6011
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

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Components

#1: Protein mono-heme c-type cytochrome ScyA / MONO-HEME FERROCYTOCHROME C


Mass: 8600.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens (bacteria) / Gene: ScyA / Plasmid: pPB10ScyA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)C41 / References: UniProt: O52685
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / 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
1113D 15N-separated NOESY
1213D 15N-separated TOCSY
1312D NOESY
1412D TOCSY
151HNHA
161HNHB
17115N-HSQC

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Sample preparation

DetailsContents: 1.5 mM Cytochrome c: 100 mM phosphate buffer; reduced with dithyonite
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 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 AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002
Bruker AVANCEBrukerAVANCE6003

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guntert, P., Mumenthaler, C., Wuthrich, K.structure solution
Amber6Caserefinement
RefinementMethod: simulated annealing in the dihedral angle space in DYANA in 15000 steps; 30 structures with the lowest target function out of a total number of 250 generated structures constitute the REM ...Method: simulated annealing in the dihedral angle space in DYANA in 15000 steps; 30 structures with the lowest target function out of a total number of 250 generated structures constitute the REM family - subject to restrained energy minimization in AMBER; the minimized mean is reported
Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 1

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