Author results

3UD6
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STRUCTURAL ANALYSES OF COVALENT ENZYME-SUBSTRATE ANALOGUE COMPLEXES REVEAL STRENGTHS AND LIMITATIONS OF DE NOVO ENZYME DESIGN
Descriptor:RETRO-ALDOLASE
Authors:Baker, D., Stoddard, B.L., Althoff, E.A., Wang, L., Jiang, L., Moody, J., Bolduc, J., Lassila, J., Hilvert, D.
Deposit date:2011-10-27
Release date:2011-11-23
Modification date:2013-11-20
Method:X-RAY DIFFRACTION (2.091 Å)
Cite:Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design.
J.Mol.Biol., 415, 2012
2LPB
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STRUCTURE OF THE COMPLEX OF THE CENTRAL ACTIVATION DOMAIN OF GCN4 BOUND TO THE MEDIATOR CO-ACTIVATOR DOMAIN 1 OF GAL11/MED15
Descriptor:Mediator of RNA polymerase II transcription subunit 15, General control protein GCN4
Authors:Brzovic, P.S., Heikaus, C.C., Kisselev, L., Vernon, R., Herbig, E., Pacheco, D., Warfield, L., Littlefield, P., Baker, D., Klevit, R.E., Hahn, S.
Deposit date:2012-02-07
Release date:2012-02-22
Method:SOLUTION NMR
Cite:The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex.
Mol.Cell, 44, 2011
2XYY
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DE NOVO MODEL OF BACTERIOPHAGE P22 PROCAPSID COAT PROTEIN
Descriptor:COAT PROTEIN
Authors:Chen, D.-H., Baker, M.L., Hryc, C.F., DiMaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W.
Deposit date:2010-11-19
Release date:2011-02-02
Modification date:2011-02-09
Method:ELECTRON MICROSCOPY (3.8 Å)
Cite:Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
2XYZ
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DE NOVO MODEL OF BACTERIOPHAGE P22 VIRION COAT PROTEIN
Descriptor:COAT PROTEIN
Authors:Chen, D.-H., Baker, M.L., Hryc, C.F., DiMaio, F., Jakana, J., Wu, W., Dougherty, M., Haase-Pettingell, C., Schmid, M.F., Jiang, W., Baker, D., King, J.A., Chiu, W.
Deposit date:2010-11-19
Release date:2011-02-02
Modification date:2011-02-09
Method:ELECTRON MICROSCOPY (4 Å)
Cite:Structural Basis for Scaffolding-Mediated Assembly and Maturation of a DsDNA Virus.
Proc.Natl.Acad.Sci.USA, 108, 2011
1YSB
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YEAST CYTOSINE DEAMINASE TRIPLE MUTANT
Descriptor:Cytosine deaminase (E.C.3.5.4.1)
Authors:Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.
Deposit date:2005-02-08
Release date:2005-05-17
Modification date:2009-02-24
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Computational thermostabilization of an enzyme.
Science, 308, 2005
1YSD
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YEAST CYTOSINE DEAMINASE DOUBLE MUTANT
Descriptor:Cytosine deaminase (E.C.3.5.4.1)
Authors:Korkegian, A., Black, M.E., Baker, D., Stoddard, B.L.
Deposit date:2005-02-08
Release date:2005-05-17
Modification date:2009-02-24
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Computational thermostabilization of an enzyme.
Science, 308, 2005
5KCI
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CRYSTAL STRUCTURE OF HTC1
Descriptor:Uncharacterized protein YPL067C
Authors:Martin, R.M., Horowitz, S., Koepnick, B., Cooper, S., Flatten, J., Rogawski, D.S., Koropatkin, N.M., Beinlich, F.R.M., Players, F., Students, U.M., Popovic, Z., Baker, D., Khatib, F., Bardwell, J.C.A.
Deposit date:2016-06-06
Release date:2016-09-21
Modification date:2016-09-28
Method:X-RAY DIFFRACTION (1.833 Å)
Cite:Determining crystal structures through crowdsourcing and coursework.
Nat Commun, 7, 2016
1VJQ
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DESIGNED PROTEIN BASED ON BACKBONE CONFORMATION OF PROCARBOXYPEPTIDASE-A (1AYE) WITH SIDECHAINS CHOSEN FOR MAXIMAL PREDICTED STABILITY.
Descriptor:DESIGNED PROTEIN
Authors:Merritt, E.A., Baker, D., Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
Deposit date:2004-03-19
Release date:2004-03-30
Modification date:2011-07-13
Method:X-RAY DIFFRACTION (2.098 Å)
Cite:Designed protein based on backbone conformation of procarboxypeptidase-A (1AYE) with sidechains chosen for maximal predicted stability.
To be Published
5IM4
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CRYSTAL STRUCTURE OF DESIGNED TWO-COMPONENT SELF-ASSEMBLING ICOSAHEDRAL CAGE I52-32
Descriptor:Designed self-assembling icosahedral cage I52-32 pentameric subunit (E.C.2.5.1.78), Designed self-assembling icosahedral cage I52-32 dimeric subunit
Authors:Liu, Y.A., Cascio, D., Sawaya, M.R., Bale, J.B., Collazo, M.J., Thomas, C., Sheffler, W., King, N.P., Baker, D., Yeates, T.O.
Deposit date:2016-03-05
Release date:2016-07-27
Modification date:2016-08-10
Method:X-RAY DIFFRACTION (3.5 Å)
Cite:Accurate design of megadalton-scale two-component icosahedral protein complexes.
Science, 353, 2016
5IM5
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CRYSTAL STRUCTURE OF DESIGNED TWO-COMPONENT SELF-ASSEMBLING ICOSAHEDRAL CAGE I53-40
Descriptor:Designed self-assembling icosahedral cage I53-40 pentameric subunit (E.C.2.5.1.9), Designed self-assembling icosahedral cage I53-40 trimeric subunit (E.C.4.1.3.16)
Authors:Liu, Y.A., Cascio, D., Sawaya, M.R., Bale, J.B., Collazo, M.J., Thomas, C., Sheffler, W., King, N.P., Baker, D., Yeates, T.O.
Deposit date:2016-03-05
Release date:2016-07-27
Modification date:2016-08-10
Method:X-RAY DIFFRACTION (3.699 Å)
Cite:Accurate design of megadalton-scale two-component icosahedral protein complexes.
Science, 353, 2016
5IM6
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CRYSTAL STRUCTURE OF DESIGNED TWO-COMPONENT SELF-ASSEMBLING ICOSAHEDRAL CAGE I32-28
Descriptor:Designed self-assembling icosahedral cage I32-28 trimeric subunit, Designed self-assembling icosahedral cage I32-28 dimeric subunit
Authors:Liu, Y.A., Cascio, D., Sawaya, M.R., Bale, J.B., Collazo, M.J., Thomas, C., Sheffler, W., King, N.P., Baker, D., Yeates, T.O.
Deposit date:2016-03-05
Release date:2016-07-27
Modification date:2016-08-10
Method:X-RAY DIFFRACTION (5.588 Å)
Cite:Accurate design of megadalton-scale two-component icosahedral protein complexes.
Science, 353, 2016
2FLD
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I-MSOI RE-DESIGNED FOR ALTERED DNA CLEAVAGE SPECIFICITY
Descriptor:PROTEIN/DNA Complex
Authors:Ashworth, J., Duarte, C.M., Havranek, J.J., Sussman, D., Monnat, R.J., Stoddard, B.L., Baker, D.
Deposit date:2006-01-05
Release date:2006-06-06
Modification date:2011-07-13
Method:X-RAY DIFFRACTION (2 Å)
Cite:Computational redesign of endonuclease DNA binding and cleavage specificity.
Nature, 441, 2006
2L69
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SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, P-LOOP NTPASE FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR28
Descriptor:OR28
Authors:Liu, G., Koga, N., Koga, R., Xiao, R., Mao, A., Mao, B., Patel, D., Ciccosanti, C., Hamilton, K., Acton, T.B., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)
Deposit date:2010-11-17
Release date:2011-01-12
Modification date:2012-02-22
Method:SOLUTION NMR
Cite:Solution NMR structure of de novo designed rossmann 2x3 fold protein, Northeast Structural Genomics Consortium Target OR28
To be Published
2LPZ
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ATOMIC MODEL OF THE TYPE-III SECRETION SYSTEM NEEDLE
Descriptor:Protein prgI
Authors:Loquet, A., Sgourakis, N.G., Gupta, R., Giller, K., Riedel, D., Goosmann, C., Griesinger, C., Kolbe, M.G., Baker, D., Becker, S., Lange, A.
Deposit date:2012-02-21
Release date:2012-05-16
Modification date:2012-06-27
Method:SOLID-STATE NMR
Cite:Atomic model of the type III secretion system needle.
Nature, 486, 2012
2MRA
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SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) TARGET OR459
Descriptor:De novo designed protein OR459
Authors:Pulavarti, S.V.S.R.K., Kipnis, Y., Sukumaran, D., Maglaqui, M., Janjua, H., Mao, L., Xiao, R., Kornhaber, G., Baker, D., Montelione, G.T., Szyperski, T., Northeast Structural Genomics Consortium (NESG)
Deposit date:2014-07-02
Release date:2014-09-17
Method:SOLUTION NMR
Cite:Solution NMR Structure of De novo designed protein, Northeast Structural Genomics Consortium (NESG) Target OR459
To be Published
3GEQ
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STRUCTURAL BASIS FOR THE CHEMICAL RESCUE OF SRC KINASE ACTIVITY
Descriptor:Proto-oncogene tyrosine-protein kinase Src (E.C.2.7.10.2)
Authors:Muratore, K.E., Seeliger, M.A., Wang, Z., Fomina, D., Neiswinger, J., Havranek, J.J., Baker, D., Kuriyan, J., Cole, P.A.
Deposit date:2009-02-25
Release date:2009-04-28
Method:X-RAY DIFFRACTION (2.2 Å)
Cite:Comparative analysis of mutant tyrosine kinase chemical rescue.
Biochemistry, 48, 2009
3NNG
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CRYSTAL STRUCTURE OF THE F5/8 TYPE C DOMAIN OF Q5LFR2_BACFN PROTEIN FROM BACTEROIDES FRAGILIS. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BFR258E
Descriptor:uncharacterized protein
Authors:Vorobiev, S., Su, M., Dimaio, F., Baker, D., Seetharaman, J., Janjua, J., Xiao, R., Ciccosanti, C., Foote, E.L., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)
Deposit date:2010-06-23
Release date:2010-08-18
Method:X-RAY DIFFRACTION (2.177 Å)
Cite:Crystal structure of the F5/8 type C domain of Q5LFR2_BACFN protein from Bacteroides fragilis.
To be Published
3NPU
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (2.25 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NPV
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (1.48 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NPW
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IN SILICO DESIGNED OF AN IMPROVED KEMP ELIMINASE KE70 MUTANT BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (2.14 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NPX
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (1.79 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NQ2
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION R2 3/5G
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (2.02 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NQ8
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION R4 8/5A
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (1.4 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NQV
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION R5 7/4A
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-29
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
3NR0
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OPTIMIZATION OF THE IN SILICO DESIGNED KEMP ELIMINASE KE70 BY COMPUTATIONAL DESIGN AND DIRECTED EVOLUTION R6 6/10A
Descriptor:deoxyribose phosphate aldolase
Authors:Khersonsky, O., Rothlisberge, D., Wollacott, A.M., Dym, O., Baker, D., Tawfik, D.S., Israel Structural Proteomics Center (ISPC)
Deposit date:2010-06-30
Release date:2011-02-09
Modification date:2014-03-19
Method:X-RAY DIFFRACTION (2.19 Å)
Cite:Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
J.Mol.Biol., 407, 2011
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