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- PDB-1a2s: THE SOLUTION NMR STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GRE... -

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Basic information

Entry
Database: PDB / ID: 1a2s
TitleTHE SOLUTION NMR STRUCTURE OF OXIDIZED CYTOCHROME C6 FROM THE GREEN ALGA MONORAPHIDIUM BRAUNII, MINIMIZED AVERAGE STRUCTURE
ComponentsCYTOCHROME C6
KeywordsELECTRON TRANSPORT / CYTOCHROME C6 / PHOTOSYSTEM I / PARAMAGNETIC NMR / SOLUTION STRUCTURE / HEME PROTEIN
Function / homology
Function and homology information


chloroplast 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 speciesMonoraphidium braunii (plant)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsBanci, L. / Bertini, I. / De La Rosa, M.A. / Koulougliotis, D. / Navarro, J.A. / Walter, O.
CitationJournal: Biochemistry / Year: 1998
Title: Solution structure of oxidized cytochrome c6 from the green alga Monoraphidium braunii.
Authors: Banci, L. / Bertini, I. / De la Rosa, M.A. / Koulougliotis, D. / Navarro, J.A. / Walter, O.
History
DepositionJan 10, 1998Processing site: BNL
Revision 1.0Apr 29, 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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

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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)9,9782
Polymers9,3591
Non-polymers6191
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 40MINIMIZED AVERAGE STRUCTURE
Representative

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Components

#1: Protein CYTOCHROME C6 / CYTOCHROME C552


Mass: 9359.270 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: OXIDIZED FORM / Source: (natural) Monoraphidium braunii (plant) / References: UniProt: Q09099
#2: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
131COSY
1411D NOE

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Sample preparation

Sample conditionspH: 5.0 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRX 500BrukerDRX 5005001
Bruker AMX 600BrukerAMX 6006002
Bruker AVANCE 800BrukerAVANCE 8008003

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Processing

Software
NameClassification
DYANAmodel building
AMBERrefinement
DYANArefinement
NMR software
NameDeveloperClassification
AmberPEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMANrefinement
DYANAstructure solution
PSEUDYANAstructure solution
Amberstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: MINIMIZED AVERAGE STRUCTURE / Conformers calculated total number: 40 / Conformers submitted total number: 1

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