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- PDB-1k3h: NMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 1k3h
TitleNMR Solution Structure of Oxidized Cytochrome c-553 from Bacillus pasteurii
Componentscytochrome c-553
KeywordsELECTRON TRANSPORT / C-553 / HEME / CYTOCHROME / BACILLUS PASTEURII / electron transfer
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding / plasma membrane
Similarity search - Function
Cytochrome c, Bacillus subtilis c550-related / : / 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 / Cytochrome c-553
Similarity search - Component
Biological speciesSporosarcina pasteurii (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, restrained energy minimization
AuthorsBanci, L. / Bertini, I. / Ciurli, S. / Dikiy, A. / Dittmer, J. / Rosato, A. / Sciara, G. / Thompsett, A.R.
Citation
Journal: Chembiochem / Year: 2002
Title: NMR solution structure, backbone mobility, and homology modeling of c-type cytochromes from gram-positive bacteria.
Authors: Banci, L. / Bertini, I. / Ciurli, S. / Dikiy, A. / Dittmer, J. / Rosato, A. / Sciara, G. / Thompsett, A.R.
#1: Journal: Biochemistry / Year: 2000
Title: Crystal Structure of Oxidized Bacillus pasteurii cytochrome c-553 at 0.97-A Resolution
Authors: Benini, S. / Gonzalez, A. / Rypniewski, W.R. / Wilson, K.S. / Van Beeumen, J.J. / Ciurli, S.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1998
Title: Modulation of Bacillus pasteurii Cytochrome c553 Reduction Potential by Structural and Solution Parameters
Authors: Benini, S. / Borsari, M. / Ciurli, S. / Dikiy, A. / Lamborghini, M.
History
DepositionOct 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_conn_type / 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 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 c-553
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7342
Polymers7,1161
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)1 / -
Representative

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Components

#1: Protein cytochrome c-553 / C553


Mass: 7115.937 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sporosarcina pasteurii (bacteria) / Plasmid: pEC86 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P82599
#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
1112D NOESY
121HNHA
1311D NOE

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Sample preparation

DetailsContents: 1-3 mM oxidized cytochrome c-553 in 10 mM phosphate buffer
Solvent system: 90%H2O+10%D2O; 100% D2O
Sample conditionsIonic strength: 10 mM phosphate buffer / pH: 7.5 / Pressure: Ambient / Temperature: 288 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
XwinNMR2.6Brukerprocessing
XEASY1.3.13Xiadata analysis
DYANA1.5Guentertstructure solution
Amber5Kollmanrefinement
RefinementMethod: torsion angle dynamics, restrained energy minimization
Software ordinal: 1
Details: PSEUDOCONTACT SHIFTS WERE INCLUDED AS CONSTRAINTS BY MEANS OF MODIFIED DYANA AND SANDER MODULES (PSEUDODYANA, PSEUDOREM) (BANCI ET AL., 1997)
NMR ensembleConformers submitted total number: 1

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