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Open data
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Basic information
Entry | Database: PDB / ID: 1yjj | ||||||
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Title | RDC-refined Solution NMR structure of oxidized putidaredoxin | ||||||
![]() | Putidaredoxin | ||||||
![]() | ELECTRON TRANSPORT / ferredoxin / [2Fe-2S] / redox / iron-sulfur / electron transfer / cytochrome P450cam | ||||||
Function / homology | ![]() P450-containing electron transport chain / 2 iron, 2 sulfur cluster binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Jain, N.U. / Tjioe, E. / Savidor, A. / Boulie, J. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 463.2 KB | Display | ![]() |
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PDB format | ![]() | 384.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.6 KB | Display | ![]() |
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Full document | ![]() | 479.3 KB | Display | |
Data in XML | ![]() | 30.8 KB | Display | |
Data in CIF | ![]() | 51.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: Protein | Mass: 11428.911 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-FES / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | 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) ...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
Details | Contents: 1 mM oxidized putidaredoxin 15N; 50 mM Tris-Cl buffer, 50 mM KCl, pH 7.4 Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 50 mM KCl / pH: 7.4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software | Name: ![]() |
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Refinement | Method: 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 representative | Selection criteria: lowest energy |
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 15 |