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- PDB-2ai5: Solution Structure of Cytochrome C552, determined by Distributed ... -

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Basic information

Entry
Database: PDB / ID: 2ai5
TitleSolution Structure of Cytochrome C552, determined by Distributed Computing Implementation for NMR data
ComponentsCytochrome c-552
KeywordsELECTRON TRANSPORT / cytochrome C / porphyrin / ferrous iron
Function / homology
Function and homology information


electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c, class ID / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Cytochrome c-552
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsNakamura, S. / Ichiki, S.I. / Takashima, H. / Uchiyama, S. / Hasegawa, J. / Kobayashi, Y. / Sambongi, Y. / Ohkubo, T.
CitationJournal: Biochemistry / Year: 2006
Title: Structure of Cytochrome c552 from a Moderate Thermophilic Bacterium, Hydrogenophilus thermoluteolus: Comparative Study on the Thermostability of Cytochrome c
Authors: Nakamura, S. / Ichiki, S.I. / Takashima, H. / Uchiyama, S. / Hasegawa, J. / Kobayashi, Y. / Sambongi, Y. / Ohkubo, T.
History
DepositionJul 29, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 c-552
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2052
Polymers8,5861
Non-polymers6191
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 / 4000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cytochrome c-552 / Cytochrome c552


Mass: 8586.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hydrogenobacter thermophilus (bacteria) / Strain: TK-6 / References: UniProt: P15452
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / 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 1H-NMR data were subjected to the structure determination using distributed computing implementations.

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Sample preparation

DetailsContents: 2mM CYTOCHROME C-552 / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM ACETATE BUFFER / pH: 4.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLORXPLOR-NIH v2.0.6Schwieters, C. D.structure solution
X-PLORXPLOR-NIH v2.0.6Schwieters, C. D.refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: Distributed Computing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 4000 / Conformers submitted total number: 20

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