1YSB
 
 | | Yeast Cytosine Deaminase Triple Mutant | | Descriptor: | CALCIUM ION, Cytosine deaminase, ZINC ION | | Authors: | Korkegian, A, Black, M.E, Baker, D, Stoddard, B.L. | | Deposit date: | 2005-02-08 | | Release date: | 2005-05-17 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Computational thermostabilization of an enzyme.
Science, 308, 2005
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8FLX
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2OST
 | | The structure of a bacterial homing endonuclease : I-Ssp6803I | | Descriptor: | CALCIUM ION, Putative endonuclease, Synthetic DNA 29 MER | | Authors: | Zhao, L, Bonocora, R.P, Shub, D.A, Stoddard, B.L. | | Deposit date: | 2007-02-06 | | Release date: | 2007-03-20 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3.1 Å) | | Cite: | The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif.
Embo J., 26, 2007
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6M9G
 | | BbvCI B2 dimer with Ta6Br14 clusters | | Descriptor: | 1,2-ETHANEDIOL, ACETATE ION, BROMIDE ION, ... | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2018-08-23 | | Release date: | 2018-11-14 | | Last modified: | 2024-05-22 | | Method: | X-RAY DIFFRACTION (2.35 Å) | | Cite: | Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.
Nucleic Acids Res., 47, 2019
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2O6M
 | | H98Q mutant of the homing endonuclease I-PPOI complexed with DNA | | Descriptor: | 5'-D(*DTP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DAP*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DA)-3', Intron-encoded endonuclease I-PpoI, MAGNESIUM ION, ... | | Authors: | Eastberg, J.H, Stoddard, B.L. | | Deposit date: | 2006-12-07 | | Release date: | 2007-10-30 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Mutability of an HNH nuclease imidazole general base and exchange of a deprotonation mechanism.
Biochemistry, 46, 2007
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2ERH
 | | Crystal Structure of the E7_G/Im7_G complex; a designed interface between the colicin E7 DNAse and the Im7 immunity protein | | Descriptor: | Colicin E7, Colicin E7 immunity protein | | Authors: | Joachimiak, L.A, Kortemme, T, Stoddard, B.L, Baker, D. | | Deposit date: | 2005-10-24 | | Release date: | 2006-07-25 | | Last modified: | 2023-08-23 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Computational Design of a New Hydrogen Bond Network and at Least a 300-fold Specificity Switch at a Protein-Protein Interface.
J.Mol.Biol., 361, 2006
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6MAG
 | | native BbvCI B2 dimer in space group C222 | | Descriptor: | ACETATE ION, BbvCI endonuclease subunit 2, GLYCEROL, ... | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2018-08-27 | | Release date: | 2018-11-14 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.
Nucleic Acids Res., 47, 2019
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4IX0
 | | Computational Design of an Unnatural Amino Acid Metalloprotein with Atomic Level Accuracy | | Descriptor: | NICKEL (II) ION, SULFATE ION, Unnatural Amino Acid Mediated Metalloprotein | | Authors: | Mills, J, Bolduc, J, Khare, S, Stoddard, B, Baker, D. | | Deposit date: | 2013-01-24 | | Release date: | 2013-08-21 | | Last modified: | 2023-11-15 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy.
J.Am.Chem.Soc., 135, 2013
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2O3K
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7JTA
 | | Crystal structure of a putative nuclease with anti-Cas9 activity from an uncultured Clostridia bacterium | | Descriptor: | (4S)-2-METHYL-2,4-PENTANEDIOL, NITRATE ION, NTF2-like nuclease/anti-CRISPR | | Authors: | Werther, R, Forsberg, K.J, Stoddard, B.L. | | Deposit date: | 2020-08-17 | | Release date: | 2021-09-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.801 Å) | | Cite: | The novel anti-CRISPR AcrIIA22 relieves DNA torsion in target plasmids and impairs SpyCas9 activity.
Plos Biol., 19, 2021
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3R3P
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4R5D
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4R5C
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8E0O
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4R6F
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3UD6
 | | Structural analyses of covalent enzyme-substrate analogue complexes reveal strengths and limitations of de novo enzyme design | | Descriptor: | 1-(6-METHOXYNAPHTHALEN-2-YL)BUTANE-1,3-DIONE, RETRO-ALDOLASE, SULFATE ION | | 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 | | Last modified: | 2023-09-13 | | 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
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3E0L
 | | Computationally Designed Ammelide Deaminase | | Descriptor: | Guanine deaminase, ZINC ION | | Authors: | Murphy, P.M, Bolduc, J.M, Gallaher, J.L, Stoddard, B.L, Baker, D. | | Deposit date: | 2008-07-31 | | Release date: | 2009-03-03 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.37 Å) | | Cite: | Alteration of enzyme specificity by computational loop remodeling and design.
Proc.Natl.Acad.Sci.USA, 106, 2009
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2FLD
 | | I-MsoI Re-Designed for Altered DNA Cleavage Specificity | | Descriptor: | 5'-D(*CP*GP*GP*AP*AP*CP*GP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*CP*TP*TP*CP*TP*GP*C)-3', 5'-D(*GP*CP*AP*GP*AP*AP*GP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*CP*GP*TP*TP*CP*CP*G)-3', CALCIUM ION, ... | | 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 | | Last modified: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Computational redesign of endonuclease DNA binding and cleavage specificity.
Nature, 441, 2006
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4R58
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8E0N
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8E0M
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8E12
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8E0L
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3E54
 | | Archaeal Intron-encoded Homing Endonuclease I-Vdi141I Complexed With DNA | | Descriptor: | DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DTP*DCP*DTP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(*DTP*DTP*DGP*DGP*DCP*DTP*DAP*DCP*DCP*DTP*DTP*DAP*DA)-3'), DNA (5'-D(P*DGP*DAP*DGP*DAP*DGP*DTP*DCP*DAP*DG)-3'), ... | | Authors: | Nomura, N, Nomura, Y, Sussman, D, Stoddard, B.L. | | Deposit date: | 2008-08-13 | | Release date: | 2008-12-30 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases
Nucleic Acids Res., 36, 2008
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8EPX
 | | Type IIS Restriction Endonuclease PaqCI, DNA bound | | Descriptor: | CALCIUM ION, DNA 1a, DNA 1b, ... | | Authors: | Kennedy, M.A, Stoddard, B.L. | | Deposit date: | 2022-10-06 | | Release date: | 2023-03-22 | | Last modified: | 2024-06-19 | | Method: | ELECTRON MICROSCOPY (3.15 Å) | | Cite: | Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI.
Nucleic Acids Res., 51, 2023
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