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- PDB-1qn0: SOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERROCYTOCHROME C3, NMR... -

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Basic information

Entry
Database: PDB / ID: 1qn0
TitleSOLUTION STRUCTURE OF DESULFOVIBRIO GIGAS FERROCYTOCHROME C3, NMR, 20 STRUCTURES
ComponentsCYTOCHROME C3
KeywordsELECTRON TRANSPORT / HEMEPROTEIN / CYTOCHROME C3 / REDOX-BOHR EFFECT / REDOX COOPERATIVITY / ENERGY TRANSDUCTION
Function / homology
Function and homology information


anaerobic respiration / 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 GIGAS (bacteria)
MethodSOLUTION NMR / RESTRAINED TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
AuthorsMessias, A.C. / Teodoro, M.L. / Brennan, L. / Legall, J. / Santos, H. / Xavier, A.V. / Turner, D.L.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structural Basis for the Network of Functional Cooperativities in Cytochrome C3 from Desulfovibrio Gigas: Solution Structures of the Oxidised and Reduced States
Authors: Brennan, L. / Turner, D.L. / Messias, A.C. / Teodoro, M.L. / Legall, J. / Santos, H. / Xavier, A.V.
#1: Journal: Biochemistry / Year: 1998
Title: Functional and Mechanistic Studies of Cytochrome C3 from Desulfovibrio Gigas: Thermodynamics of a 'Proton Thruster'
Authors: Louro, R.O. / Catarino, T. / Turner, D.L. / Picarra-Pereira, M.A. / Pacheco, I. / Legall, J. / Xavier, A.V.
#2: Journal: Protein Sci. / Year: 1996
Title: Cytochromes C3 from Desulfovibrio Gigas: Crystal Structure at 1.8 A Resolution and Evidence for a Specific Calcium-Binding Site
Authors: Matias, P.M. / Morais, J. / Carrondo, M.A. / Wilson, K. / Dauter, Z. / Sieker, L.
History
DepositionOct 11, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: pdbx_database_status / struct_conn / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_mr / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4915
Polymers12,0171
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
RepresentativeModel #1

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Components

#1: Protein CYTOCHROME C3 / TETRAHEME CYTOCHROME


Mass: 12016.550 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 GIGAS (bacteria) / Cellular location: PERIPLASM / References: UniProt: P00133
#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
Has protein modificationY
Sequence detailsRESIDUE 40 WAS FOUND TO BE GLN

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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

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Sample preparation

Sample conditionspH: 7.3 / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameDeveloperClassification
INDYANAD.L.TURNERrefinement
INDYANAstructure solution
RefinementMethod: RESTRAINED TORSION ANGLE DYNAMICS WITH SIMULATED ANNEALING
Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION MENTIONED. INDYANA REFERENCE:D.L.TURNER, L.BRENNAN,H.E.MEYER,C.LOHAUS, C.SIETHOFF,H.S.COSTA,B.GONZALEZ, H.SANTOS,J.E.SUAREZ(1999) EUR.J.BIOCHEM., 264,833-839.
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 600 / Conformers submitted total number: 20

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