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- PDB-2pcf: THE COMPLEX OF CYTOCHROME F AND PLASTOCYANIN DETERMINED WITH PARA... -

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Basic information

Entry
Database: PDB / ID: 2pcf
TitleTHE COMPLEX OF CYTOCHROME F AND PLASTOCYANIN DETERMINED WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES
Components
  • CYTOCHROME F
  • PLASTOCYANIN
KeywordsCOMPLEX (ELECTRON TRANSPORT PROTEINS) / ELECTRON TRANSPORT / PARAMAGNETIC / CHEMICAL SHIFT / COMPLEX FORMATION / DYNAMIC COMPLEX / PHOTOSYNTHESIS / PSEUDOCONTACT SHIFT
Function / homology
Function and homology information


: / chloroplast thylakoid lumen / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / copper ion binding / heme binding
Similarity search - Function
Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type ...Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Plastocyanin / Blue (type 1) copper protein, plastocyanin-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rudiment single hybrid motif / Cupredoxins - blue copper proteins / Cupredoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Plastocyanin, chloroplastic / Cytochrome f
Similarity search - Component
Biological speciesSpinacia oleracea (spinach)
Brassica rapa (field mustard)
MethodSOLUTION NMR / DYNAMICS
AuthorsUbbink, M. / Ejdeback, M. / Karlsson, B.G. / Bendall, D.S.
Citation
Journal: Structure / Year: 1998
Title: The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics.
Authors: Ubbink, M. / Ejdeback, M. / Karlsson, B.G. / Bendall, D.S.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: Effects of Codon Usage and Vector-Host Combinations on the Expression of Spinach Plastocyanin in Escherichia Coli
Authors: Ejdeback, M. / Young, S. / Samuelsson, A. / Karlsson, B.G.
#2: Journal: Structure / Year: 1994
Title: Crystal Structure of Chloroplast Cytochrome F Reveals a Novel Cytochrome Fold and Unexpected Heme Ligation
Authors: Martinez, S.E. / Huang, D. / Szczepaniak, A. / Cramer, W.A. / Smith, J.L.
History
DepositionDec 22, 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 1.3Mar 16, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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_asym_id / _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_asym_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 23, 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: PLASTOCYANIN
B: CYTOCHROME F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4214
Polymers37,7392
Non-polymers6822
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 9999REFER TO PUBLICATION
Representative

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Components

#1: Protein PLASTOCYANIN


Mass: 10420.557 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spinacia oleracea (spinach) / Cellular location: THYLAKOID LUMEN / Gene: PETE / Organelle: CHLOROPLAST / Plasmid: PSY2 / Species (production host): Escherichia coli / Cellular location (production host): PERIPLASM / Gene (production host): PETE / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00289
#2: Protein CYTOCHROME F


Mass: 27318.189 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa (field mustard) / Cellular location: THYLAKOID MEMBRANE / Gene: PETE / Organelle: CHLOROPLAST / Plasmid: PSY2 / Species (production host): Escherichia coli / Gene (production host): PETE / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36438
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#4: 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: 15N-HSQC

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Sample preparation

Sample conditionspH: 6 / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMBrukerAM5001
Varian UNITYVarianUNITY5002
Varian UNITYPLUSVarianUNITYPLUS6003

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1structure solution
RefinementMethod: DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND BELOW AND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: REFER TO PUBLICATION / Conformers calculated total number: 9999 / Conformers submitted total number: 10

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