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- PDB-2jxm: Ensemble of twenty structures of the Prochlorothrix hollandica pl... -

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Basic information

Entry
Database: PDB / ID: 2jxm
TitleEnsemble of twenty structures of the Prochlorothrix hollandica plastocyanin- cytochrome f complex
Components
  • Cytochrome f
  • Plastocyanin
KeywordsELECTRON TRANSPORT / Copper / Metal-binding / Transport
Function / homology
Function and homology information


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 / 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 ...Plastocyanin, cyanobacteria / Cytochrome f large domain / 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 / Cytochrome f
Similarity search - Component
Biological speciesProchlorothrix hollandica (bacteria)
MethodSOLUTION NMR / Rigid Body docking, Energy minimisation
AuthorsHulsker, R. / Baranova, M. / Bullerjahn, G. / Ubbink, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Dynamics in the transient complex of plastocyanin-cytochrome f from Prochlorothrix hollandica.
Authors: Hulsker, R. / Baranova, M.V. / Bullerjahn, G.S. / Ubbink, M.
History
DepositionNov 22, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)37,4424
Polymers36,7602
Non-polymers6822
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Plastocyanin


Mass: 10148.560 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorothrix hollandica (bacteria) / Gene: petE / Production host: Escherichia coli (E. coli) / References: UniProt: P50057
#2: Protein Cytochrome f


Mass: 26611.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prochlorothrix hollandica (bacteria) / Gene: petA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RN59
#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: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 85 uM [U-99% 15N] plastocyanin, 50 uM cytochrome f, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
85 uMplastocyanin[U-99% 15N]1
50 uMcytochrome f1
Sample conditionsIonic strength: 10 / pH: 6 / Pressure: ambient / Temperature: 300 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
NameDeveloperClassification
TopSpinBruker Biospincollection
AzaraBoucher, W.processing
AzaraBoucher, W.data analysis
ANSIGKraulis, P.J.processing
ANSIGKraulis, P.J.data analysis
X-PLOR NIHSchwieters, C.D. et al.refinement
RefinementMethod: Rigid Body docking, Energy minimisation / Software ordinal: 1
Details: Rigid Body docking based on PDB entry 1B3I and a homology model of cytochrome f. Docking energies based on pseudocontact and chemical shift perturbation restraints. Energy minimisation of side-chains.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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