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Open data
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Basic information
Entry | Database: PDB / ID: 2mi7 | ||||||
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Title | Solution NMR structure of alpha3Y | ||||||
![]() | de novo protein a3Y | ||||||
![]() | DE NOVO PROTEIN / three-helix bundle / redox protein / tyrosine radical / proton-coupled electron transfer | ||||||
Function / homology | Designed single chain three-helix bundle / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Mainly Alpha![]() | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Glover, S.D. / Jorge, C. / Liang, L. / Valentine, K.G. / Hammarstrom, L. / Tommos, C. | ||||||
![]() | ![]() Title: Photochemical tyrosine oxidation in the structurally well-defined alpha 3Y protein: proton-coupled electron transfer and a long-lived tyrosine radical. Authors: Glover, S.D. / Jorge, C. / Liang, L. / Valentine, K.G. / Hammarstrom, L. / Tommos, C. #1: Journal: Biochemistry / Year: 1999 Title: De novo proteins as models of radical enzymes. Authors: Tommos, C. / Skalicky, J.J. / Pilloud, D.L. / Wand, A.J. / Dutton, P.L. #2: ![]() Title: Structure of a de novo designed protein model of radical enzymes. Authors: Dai, Q.H. / Tommos, C. / Fuentes, E.J. / Blomberg, M.R. / Dutton, P.L. / Wand, A.J. #3: Journal: J.Am.Chem.Soc. / Year: 2011 Title: Electrochemical and structural properties of a protein system designed to generate tyrosine Pourbaix diagrams. Authors: Martinez-Rivera, M.C. / Berry, B.W. / Valentine, K.G. / Westerlund, K. / Hay, S. / Tommos, C. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Reversible voltammograms and a Pourbaix diagram for a protein tyrosine radical. Authors: Berry, B.W. / Martinez-Rivera, M.C. / Tommos, C. #5: ![]() Title: Reversible phenol oxidation and reduction in the structurally well-defined 2-Mercaptophenol-alpha 3C protein. Authors: Tommos, C. / Valentine, K.G. / Martinez-Rivera, M.C. / Liang, L. / Moorman, V.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 673.1 KB | Display | ![]() |
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PDB format | ![]() | 568.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.4 KB | Display | ![]() |
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Full document | ![]() | 650.6 KB | Display | |
Data in XML | ![]() | 40 KB | Display | |
Data in CIF | ![]() | 63.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 7539.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET32b / Production host: ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
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Sample |
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Sample conditions | Ionic strength: 60 / pH: 5.6 / Pressure: ambient / Temperature: 303 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||
NMR constraints | NOE constraints total: 784 / NOE intraresidue total count: 221 / NOE long range total count: 165 / NOE medium range total count: 214 / NOE sequential total count: 184 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 54 / Protein psi angle constraints total count: 52 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.153 ° Conformer selection criteria: NOE violation cutoff >0.1A, bb dihedral angle violation cutoff >2 degrees, then lowest energy Conformers calculated total number: 1000 / Conformers submitted total number: 32 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 1.037 ° / Maximum upper distance constraint violation: 0.094 Å / Torsion angle constraint violation method: sum of r^-6 | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.0058 Å / Distance rms dev error: 0.0005 Å |