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- PDB-1c6s: THE SOLUTION STRUCTURE OF CYTOCHROME C6 FROM THE THERMOPHILIC CYA... -

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Basic information

Entry
Database: PDB / ID: 1c6s
TitleTHE SOLUTION STRUCTURE OF CYTOCHROME C6 FROM THE THERMOPHILIC CYANOBACTERIUM SYNECHOCOCCUS ELONGATUS, NMR, 20 STRUCTURES
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT / CYTOCHROME C6 / PHOTOSYNTHESIS / SYNECHOCOCCUS ELONGATUS
Function / homology
Function and homology information


plasma membrane-derived thylakoid lumen / photosynthesis / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome c6 / Cytochrome c, class IC / Cytochrome C oxidase, cbb3-type, subunit III / 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 c6
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsRoesch, P. / Beissinger, M. / Sticht, H. / Sutter, M. / Ejchart, A. / Haehnel, W.
Citation
Journal: EMBO J. / Year: 1998
Title: Solution structure of cytochrome c6 from the thermophilic cyanobacterium Synechococcus elongatus.
Authors: Beissinger, M. / Sticht, H. / Sutter, M. / Ejchart, A. / Haehnel, W. / Rosch, P.
History
DepositionMar 31, 1997Processing site: BNL
Revision 1.0Apr 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_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 / _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 16, 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 C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8062
Polymers9,1871
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 / 50ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Representative

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Components

#1: Protein CYTOCHROME C6 / CYTOCHROME C553


Mass: 9187.367 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: REDUCED / Source: (natural) Synechococcus elongatus (bacteria) / References: UniProt: P0A3Y0
#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

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
NDEEstructure solution
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
NMR ensembleConformer selection criteria: ENERGY, AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 50 / Conformers submitted total number: 20

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