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- PDB-1lm2: NMR structural characterization of the reduction of chromium(VI) ... -

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Basic information

Entry
Database: PDB / ID: 1lm2
TitleNMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c7
Componentscytochrome c7
KeywordsELECTRON TRANSPORT / chromium / cytochrome c7
Function / homology
Function and homology information


anaerobic respiration / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Cytochrome c7 and related cytochrome c / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
CHROMIUM ION / HEME C / Cytochrome c3
Similarity search - Component
Biological speciesDesulfuromonas acetoxidans (bacteria)
MethodSOLUTION NMR / simulated annealing in torsion angle space
AuthorsAssfalg, M. / Bertini, I. / Bruschi, M. / Michel, C. / Turano, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: The metal reductase activity of some multiheme cytochromes c: NMR structural characterization of the reduction of chromium(VI) to chromium(III) by cytochrome c(7).
Authors: Assfalg, M. / Bertini, I. / Bruschi, M. / Michel, C. / Turano, P.
History
DepositionApr 30, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / 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 / _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 c7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1885
Polymers7,2801
Non-polymers1,9084
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)35 / 500structures with best target function
RepresentativeModel #1fewest violations

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Components

#1: Protein cytochrome c7 / Cytochrome c3 / Cytochrome c551.5


Mass: 7280.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfuromonas acetoxidans (bacteria) / References: UniProt: P00137
#2: Chemical ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cr
#3: 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
NMR detailsText: The protein solution was titrated by addition of increasing amounts of the (CrO4)2- solution directly in the NMR tube. The (CrO4)2- solution was kept under argon atmosphere to avoid the ...Text: The protein solution was titrated by addition of increasing amounts of the (CrO4)2- solution directly in the NMR tube. The (CrO4)2- solution was kept under argon atmosphere to avoid the presence of oxygen in the NMR tube.

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Sample preparation

DetailsContents: 2 mM cytochrome c7-chromium(III) / Solvent system: 90% H2O, 10% D2O; 100 mM phosphate buffer
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 DRX / Manufacturer: Bruker / Model: DRX / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
DYANA1.5Guentertstructure solution
DYANA1.5Guentertrefinement
RefinementMethod: simulated annealing in torsion angle space / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with best target function
Conformers calculated total number: 500 / Conformers submitted total number: 35

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