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- PDB-1a2i: SOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERR... -

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Entry
Database: PDB / ID: 1a2i
TitleSOLUTION STRUCTURE OF DESULFOVIBRIO VULGARIS (HILDENBOROUGH) FERROCYTOCHROME C3, NMR, 20 STRUCTURES
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / HEMEPROTEIN / ELECTRON TRANSFER / REDOX-BOHR EFFECT / COOPERATIVITY / ENERGY TRANSDUCTION
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 subsp. vulgaris str. Hildenborough (bacteria)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS WITH SIMULATED ANNEALING
AuthorsMessias, A.C. / Kastrau, D.H.K. / Costa, H.S. / Legall, J. / Turner, D.L. / Santos, H. / Xavier, A.V.
Citation
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. / Costa, H.S. / LeGall, J. / Turner, D.L. / Santos, H. / Xavier, A.V.
#1: Journal: To be Published
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.
#2: Journal: J.Biol.Inorg.Chem. / Year: 1997
Title: Redox-Bohr Effect in Electron/Proton Energy Transduction: Cytochrome C3 Coupled to Hydrogenase Works as a 'Proton Thruster' in Desulfovibrio Vulgaris
Authors: Louro, R.O. / Catarino, T. / Legall, J. / Xavier, A.V.
#3: Journal: Eur.J.Biochem. / Year: 1996
Title: NMR Studies of Cooperativity in the Tetrahaem Cytochrome C3 from Desulfovibrio Vulgaris
Authors: Turner, D.L. / Salgueiro, C.A. / Catarino, T. / Legall, J. / Xavier, A.V.
History
DepositionJan 5, 1998Processing site: BNL
Revision 1.0Jul 8, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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 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 / 600LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein CYTOCHROME C3 / TETRAHEME CYTOCHROME


Mass: 11687.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CLASS III OF C-TYPE CYTOCHROMES, FULLY REDUCED FORM
Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria)
Cellular location: PERIPLASM / Species: Desulfovibrio vulgaris / 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D-1H-NOESY 2D-1H-TOCSY 2D-1H-COSY

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Sample preparation

Sample conditionspH: 8.5 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz

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Processing

Software
NameClassification
DYANAmodel building
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT,WUTHRICHrefinement
DYANAstructure solution
RefinementMethod: RESTRAINED MOLECULAR 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: 600 / Conformers submitted total number: 20

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