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- PDB-2bpn: SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERR... -

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Basic information

Entry
Database: PDB / ID: 2bpn
TitleSOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERRICYTOCHROME C3, NMR, 20 STRUCTURES
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / HEMEPROTEIN / CYTOCHROME C3 / REDOX COOPERATIVITY / REDOX-BOHR COOPERATIVITY / TRANSDUCTION / PARAMAGNETIC
Function / homology
Function and homology information


anaerobic respiration / periplasmic space / electron transfer activity / 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 c family profile. / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsMessias, A.C. / Aguiar, A.P. / Brennan, L. / Xavier, A.V. / Turner, D.L.
Citation
Journal: Biochim.Biophys.Acta / Year: 2006
Title: Solution Structures of Tetrahaem Ferricytochrome C(3) from Desulfovibrio Vulgaris (Hildenborough) and its K45Q Mutant: The Molecular Basis of Cooperativity.
Authors: Messias, A.C. / Aguiar, A.P. / Brennan, L. / Salgueiro, C.A. / Saraiva, L.M. / Xavier, A.V. / Turner, D.L.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Solution Structure of Desulfovibrio Vulgaris (Hildenborough) Ferrocytochrome C3: Structural Basis for Functional Cooperativity.
Authors: Messias, A.C. / Kastrau, D.H.W. / Costa, H.S. / Legall, J. / Turner, D.L. / Santos, H. / Xavier, A.V.
#2: Journal: Inorg.Chim.Acta. / Year: 1998
Title: Refinement of the Three-Dimensional Structures of Cytochromes C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 A Resolution and from Desulfovibrio Desulfuricans Atcc27774 at 1.6 A Resolution
Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A.
History
DepositionApr 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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 / 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_entry_details.has_protein_modification / _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_auth_seq_id / _struct_conn.ptnr2_label_asym_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

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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)14,1615
Polymers11,6871
Non-polymers2,4744
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 155LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein CYTOCHROME C3


Mass: 11687.463 Da / Num. of mol.: 1 / Fragment: CYTOCHROME C3, RESIDUES 23-129 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P00131
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Compound detailsPARTICIPATES IN SULFATE RESPIRATION COUPLED WITH PHOSPHORYLATION BY TRANSFERRING ELECTRONS FROM THE ...PARTICIPATES IN SULFATE RESPIRATION COUPLED WITH PHOSPHORYLATION BY TRANSFERRING ELECTRONS FROM THE ENZYME DEHYDROGENASE TO FERREDOXIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D-1H-NOESY
1212D-1H-TOCSY
1312D-1H-COSY
NMR detailsText: NONE

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Sample preparation

DetailsContents: 92% WATER/8% D2O AND 100% D2O
Sample conditionspH: 7.1 / Temperature: 303.0 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
PARADYANAD.L.TURNER,L,BRENNAN,S.G.CHAMBERLIN, R.O.LOURO, A.V.XAVIERrefinement
PARADYANAstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 155 / Conformers submitted total number: 20

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