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- PDB-1tu2: THE COMPLEX OF NOSTOC CYTOCHROME F AND PLASTOCYANIN DETERMIN WITH... -

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Basic information

Entry
Database: PDB / ID: 1tu2
TitleTHE COMPLEX OF NOSTOC CYTOCHROME F AND PLASTOCYANIN DETERMIN WITH PARAMAGNETIC NMR. BASED ON THE STRUCTURES OF CYTOCHROME F AND PLASTOCYANIN, 10 STRUCTURES
Components
  • Apocytochrome f
  • Plastocyanin
KeywordsELECTRON TRANSPORT / PARAMAGNETIC / CHEMICAL SHIFT / COMPLEX FORMATION / DYNAMIC COMPLEX / PHOTOSYNTHESIS / PSEUDOCONTACT SHIFT / ELECTRON TRANSPORT PROTEINS COMPLEX
Function / homology
Function and homology information


electron transporter, transferring electrons from cytochrome b6/f complex of photosystem II activity / plasma membrane-derived thylakoid membrane / photosynthesis / electron transfer activity / iron ion binding / copper ion binding / heme binding
Similarity search - Function
Plastocyanin, cyanobacteria / 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 ...Plastocyanin, cyanobacteria / 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 / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Blue (type 1) copper protein, binding site / Type-1 copper (blue) proteins signature. / Rudiment single hybrid motif / Cupredoxins - blue copper proteins / Cupredoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / HEME C / Plastocyanin / Cytochrome f
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodSOLUTION NMR / DYNAMICS
AuthorsDiaz-Moreno, I. / Diaz-Quintana, A. / De la Rosa, M.A. / Ubbink, M.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Structure of the complex between plastocyanin and cytochrome f from the cyanobacterium Nostoc sp. PCC 7119 as determined by paramagnetic NMR. The balance between electrostatic and hydrophobic ...Title: Structure of the complex between plastocyanin and cytochrome f from the cyanobacterium Nostoc sp. PCC 7119 as determined by paramagnetic NMR. The balance between electrostatic and hydrophobic interactions within the transient complex determines the relative orientation of the two proteins.
Authors: Diaz-Moreno, I. / Diaz-Quintana, A. / De la Rosa, M.A. / Ubbink, M.
#1: Journal: To be Published
Title: Plastocyanin from Nostoc sp. PCC 7119 Uses the Same Electrostatic and Hydrophobic Surface Areas for the Interaction with both Cytochrome f and Photosystem I
Authors: Molina-Heredia, F.P. / Hervas, M. / Navarro, J.A. / De la Rosa, M.A.
#2: Journal: BIOCHEM.BIOPHYS.RES.COMMUN. / Year: 1998
Title: Cloning and correct expression in Escherichia coli of the petE and petJ genes respectively encoding plastocyanin and cytochrome c6 from the cyanobacterium Anabaena sp. PCC 7119
Authors: Molina-Heredia, F.P. / Hervas, M. / Navarro, J.A. / De la Rosa, M.A.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plastocyanin
B: Apocytochrome f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0444
Polymers38,3622
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 / 5000REFER TO PUBLICATION
RepresentativeModel #3closest to the average

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Components

#1: Protein Plastocyanin


Mass: 11116.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Cellular location: THYLAKOID LUMEN / Gene: PETE / Organelle: THYLACOID / Plasmid: PEAP-WT / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P46444
#2: Protein Apocytochrome f


Mass: 27245.305 Da / Num. of mol.: 1 / Fragment: SOLUBLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7119 / Cellular location: THYLAKOID MEMBRANE / Gene: PETA / Organelle: THYLACOID / Plasmid: PEAF-WT / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: Q93SW9
#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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 15N-HSQC
NMR detailsText: SYSTEM: 95% BUFFER (10 MM SODIUM PHOSPHATE) 5% D2O CADMIUM(II)-SUBSTITUTED 15N PLASTOCYANIN AND UNLABELED CYTOCHROME F WERE USED.

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Sample preparation

Sample conditionsIonic strength: 10mM / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.851refinement
ANSIG3.3KRAULISdata analysis
Azara2.7BOUCHERprocessing
XwinNMR3.1collection
RefinementMethod: DYNAMICS / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND BELOW AND IN THE JRNL CITATION ABOVE.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: REFER TO PUBLICATION / Conformers calculated total number: 5000 / Conformers submitted total number: 10

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