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- PDB-1tkw: The transient complex of poplar plastocyanin with turnip cytochro... -

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Basic information

Entry
Database: PDB / ID: 1tkw
TitleThe transient complex of poplar plastocyanin with turnip cytochrome f determined with paramagnetic NMR
Components
  • Cytochrome f
  • Plastocyanin A
KeywordsPHOTOSYNTHESIS / Electron transfer / paramagnetic / rigid body calculations
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 A, chloroplastic / Cytochrome f
Similarity search - Component
Biological speciesPopulus nigra (black poplar)
Brassica rapa subsp. rapa (turnip)
MethodSOLUTION NMR / Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints.
AuthorsLange, C. / Cornvik, T. / Diaz-Moreno, I. / Ubbink, M.
CitationJournal: Biochim.Biophys.Acta / Year: 2005
Title: The transient complex of poplar plastocyanin with cytochrome f: effects of ionic strength and pH
Authors: Lange, C. / Cornvik, T. / Diaz-Moreno, I. / Ubbink, M.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 1.4Nov 13, 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

Downloads & links

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Assembly

Deposited unit
A: Plastocyanin A
B: Cytochrome f
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7214
Polymers38,0392
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 / 104structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Plastocyanin A


Mass: 10493.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Populus nigra (black poplar) / Gene: PETE / Plasmid: pETPC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00299
#2: Protein Cytochrome f


Mass: 27545.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica rapa subsp. rapa (turnip) / Species: Brassica rapa / Strain: subsp. rapa / Gene: PETA / Plasmid: pTC1 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / 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 experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 15N HSQC
2222D 15N HSQC
NMR detailsText: This structure was determined using the XRD structures of plastocyanin and cytochrome f, docked on the basis of intermolecular pseudocontact shifts and chemical shift perturbations due to binding.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in oxidized state in 10 mM sodium phosphate pH 6.094% H2O, 6% D2O
20.5 mM Cd-substituted poplar plastocyanin + 0.35 mM soluble fragment of turnip cytochrome f in reduced state in 10 mM sodium phosphate pH 6.0 + 1 mM sodium ascorbate94% H2O, 6% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
110 mM 61 atm303 K
211 mM 61 atm303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
Azara2.7W. Boucherprocessing
ANSIGAnsig-for-Windows 1.02P. Kraulis, M. Helgstranddata analysis
X-PLORXPLOR-NIH 2.9.1structure solution
X-PLORXPLOR-NIH 2.9.1refinement
RefinementMethod: Rigid body docking using intermolecular pseudocontact shifts restraints, chemical shift perturbation restraints, electrostatic restraints.
Software ordinal: 1
Details: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 ...Details: The structures are based on 38 chemical shift perturbation restraints, 42 pseudocontact shifts restraints, 42 pseudocontact angle restraints, 120 minimal distance restraints and 4 electrostatic restraints. Backbone RMSD (in Angstrom) with the mean for each model: 1: 1.28, 2: 2.26, 3: 1.29, 4: 3.12, 5: 1.52, 6: 1.49, 7: 3.68, 8: 2.68, 9: 1.58, 10: 3.43, average=2.23+/-0.88
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 104 / Conformers submitted total number: 10

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