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Open data
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Basic information
Entry | Database: PDB / ID: 5jhi | ||||||
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Title | Solution structure of the de novo mini protein gEHE_06 | ||||||
![]() | W35 | ||||||
![]() | DE NOVO PROTEIN | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / molecular dynamics | ||||||
![]() | Buchko, G.W. / Bahl, C.D. / Gilmore, J.M. / Pulavarti, S.V. / Baker, D. / Szyperski, T. | ||||||
![]() | ![]() Title: Accurate de novo design of hyperstable constrained peptides. Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P. ...Authors: Bhardwaj, G. / Mulligan, V.K. / Bahl, C.D. / Gilmore, J.M. / Harvey, P.J. / Cheneval, O. / Buchko, G.W. / Pulavarti, S.V. / Kaas, Q. / Eletsky, A. / Huang, P.S. / Johnsen, W.A. / Greisen, P.J. / Rocklin, G.J. / Song, Y. / Linsky, T.W. / Watkins, A. / Rettie, S.A. / Xu, X. / Carter, L.P. / Bonneau, R. / Olson, J.M. / Coutsias, E. / Correnti, C.E. / Szyperski, T. / Craik, D.J. / Baker, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.1 KB | Display | ![]() |
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PDB format | ![]() | 209.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.4 KB | Display | ![]() |
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Full document | ![]() | 582.2 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nd2C ![]() 2nd3C ![]() 5jg9C ![]() 5ji4C ![]() 5kvnC ![]() 5kwoC ![]() 5kwpC ![]() 5kwxC ![]() 5kwzC ![]() 5kx0C ![]() 5kx1C ![]() 5kx2C C: citing same article ( |
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Similar structure data | |
Other databases |
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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/peptide | Mass: 4278.767 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / 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
Details | Type: solution Contents: 50 mM sodium chloride, 25 mM sodium acetate, 1 mM [U-99% 15N] W35, 93% H2O/7% D2O Label: W35 / Solvent system: 93% H2O/7% D2O | ||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 75 mM / Ionic strength err: 3 / PH err: 0.2 / Pressure: 1 atm / Temperature: 293 K / Temperature err: 0.5
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-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 2 Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION ...Details: STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY USING CYANA (AUTOMATED NOESY ASSIGNMENTS). A TOTAL OF 20 STRUCTURES OUT OF 100 WITH LOWEST TARGET FUNCTION FROM THE FINAL CYANA CALCULATION WERE TAKEN AND REFINED BY RESTRAINED MOLECULAR DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) AFTER ADDING 1% TO THE UPPER BOUNDARY LIMIT OF THE DISTANCE RESTRAINTS AND THE VDW LIMIT TO THE LOWER RESTRAINT. PARAM19 WAS USED FOR THE WATER REFINEMENT CALCULATIONS | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |