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- PDB-1l3o: SOLUTION STRUCTURE DETERMINATION OF THE FULLY OXIDIZED DOUBLE MUT... -

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Basic information

Entry
Database: PDB / ID: 1l3o
TitleSOLUTION STRUCTURE DETERMINATION OF THE FULLY OXIDIZED DOUBLE MUTANT K9-10A CYTOCHROME C7 FROM DESULFUROMONAS ACETOXIDANS, ENSEMBLE OF 35 STRUCTURES
Componentscytochrome c7
KeywordsOXYGEN STORAGE/TRANSPORT / automatic assignment / cytochrome c7 / electron transfer / multiheme cytochromes / NMR solution structures / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDesulfuromonas acetoxidans (bacteria)
MethodSOLUTION NMR / simulated annealing in torsion angle space, restrained energy minimization
AuthorsAssfalg, M. / Bertini, I. / Turano, P. / Bruschi, M. / Durand, M.C. / Giudici-Orticoni, M.T. / Dolla, A.
CitationJournal: J.Biomol.NMR / Year: 2002
Title: A quick solution structure determination of the fully oxidized double mutant K9-10A cytochrome c7 from Desulfuromonas acetoxidans and mechanistic implications.
Authors: Assfalg, M. / Bertini, I. / Turano, P. / Bruschi, M. / Durand, M.C. / Giudici-Orticoni, M.T. / Dolla, A.
History
DepositionFeb 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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_conn_angle / 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 / _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_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_ref_seq_dif.details / _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 c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0204
Polymers7,1641
Non-polymers1,8563
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 500The submitted conformer models are the 35 structures with the lowest target function values
Representative

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Components

#1: Protein cytochrome c7 / CYTOCHROME C3 / CYTOCHROME C551.5


Mass: 7164.105 Da / Num. of mol.: 1 / Mutation: K9A, K10A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfuromonas acetoxidans (bacteria) / Production host: Desulfovibrio desulfuricans (bacteria) / Strain (production host): G201 / References: UniProt: P00137
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / 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 NOESY

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Sample preparation

DetailsContents: 2mM cytochrome c7
Solvent system: 100mM phosphate buffer; pH 6.5; 90% H2O, 10% D2O
Sample conditionsIonic strength: 100 mM phosphate buffer / pH: 6.5 / Pressure: 1 atm / 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 spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
PSEUDYANA1.5Guentert, P., Wuethrich, K.structure solution
Amber5Kolman, Caserefinement
RefinementMethod: simulated annealing in torsion angle space, restrained energy minimization
Software ordinal: 1
NMR ensembleConformer selection criteria: The submitted conformer models are the 35 structures with the lowest target function values
Conformers calculated total number: 500 / Conformers submitted total number: 35

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