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- PDB-1yjj: RDC-refined Solution NMR structure of oxidized putidaredoxin -

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Basic information

Entry
Database: PDB / ID: 1yjj
TitleRDC-refined Solution NMR structure of oxidized putidaredoxin
ComponentsPutidaredoxin
KeywordsELECTRON TRANSPORT / ferredoxin / [2Fe-2S] / redox / iron-sulfur / electron transfer / cytochrome P450cam
Function / homology
Function and homology information


P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp domain superfamily / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsJain, N.U. / Tjioe, E. / Savidor, A. / Boulie, J.
Citation
Journal: Biochemistry / Year: 2005
Title: Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings.
Authors: Jain, N.U. / Tjioe, E. / Savidor, A. / Boulie, J.
#1: Journal: Biochemistry / Year: 1999
Title: A refined model for the solution structure of oxidized putidaredoxin
Authors: Pochapsky, T.C. / Jain, N.U. / Kuti, M. / Lyons, T.A. / Heymont, J.
#2: Journal: Structure / Year: 1998
Title: New aspects of electron transfer revealed by the crystal structure of a truncated bovine adrenodoxin, ADX(4-108)
Authors: MULLER, A. / MULLER, J.J. / MULLER, Y.A. / UHLMANN, H. / BERNHARDT, R. / HEINEMANN, U.
#3: Journal: Biochemistry / Year: 1994
Title: An NMR-derived model for the solution structure of oxidized putidaredoxin, a 2Fe-2S Ferredoxin from pseudomonas
Authors: POCHAPSKY, T.C. / YE, X.M. / RATNASWAMY, G. / LYONS, T.A.
#4: Journal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of putidaredoxin, the [2Fe-2S] component of the P450cam monooxygenase system from Pseudomonas putida
Authors: Sevrioukova, I.F. / Garcia, C. / Li, H. / Bhaskar, B. / Poulos, T.L.
History
DepositionJan 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 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: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,6052
Polymers11,4291
Non-polymers1761
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 50structures with the lowest energy
RepresentativeModel #2lowest energy

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Components

#1: Protein Putidaredoxin / PDX


Mass: 11428.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pkM536 / Production host: Escherichia coli (E. coli) / Strain (production host): NCM533 / References: UniProt: P00259
#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-coupled 2D 15N-1H HSQC; 7.5% bicelle (DMPC:DHPC-2.9:1)
12115N-coupled 2D 15N-1H HSQC; 10 mg/mL Phage
NMR detailsText: The structures were refined against 15N-1H RDC restraints using previously published NOE and dihedral angle restraints for Pdx. The restraints for the metal binding loop (residues 36-48,85-86) ...Text: The structures were refined against 15N-1H RDC restraints using previously published NOE and dihedral angle restraints for Pdx. The restraints for the metal binding loop (residues 36-48,85-86) were modeled from bovine adrenodoxin crystal structure.

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Sample preparation

DetailsContents: 1 mM oxidized putidaredoxin 15N; 50 mM Tris-Cl buffer, 50 mM KCl, pH 7.4
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM KCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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Processing

NMR softwareName: Xplor-NIH / Version: 2.9.6 / Developer: Schwieters, Kuszewski, Tjandra, Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on 1239 NOE restriants, 160 dihedral angle restraints and 155 RDC restraints, 28 paramagnetic distance restraints from relaxation measurements and 18 distance ...Details: The structures are based on 1239 NOE restriants, 160 dihedral angle restraints and 155 RDC restraints, 28 paramagnetic distance restraints from relaxation measurements and 18 distance restriants from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 15

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