1U0D
 
 | | Y33H Mutant of Homing endonuclease I-CreI | | Descriptor: | 5'-D(*CP*GP*GP*AP*AP*CP*TP*GP*TP*CP*TP*CP*AP*CP*GP*AP*CP*GP*TP*TP*TP*CP*GP*C)-3', 5'-D(*GP*CP*GP*AP*AP*AP*CP*GP*TP*CP*GP*TP*GP*AP*GP*AP*CP*AP*GP*TP*TP*CP*CP*G)-3', DNA endonuclease I-CreI | | Authors: | Sussman, D, Chadsey, M, Fauce, S, Engel, A, Bruett, A, Monnat, R, Stoddard, B.L, Seligman, L.M. | | Deposit date: | 2004-07-13 | | Release date: | 2004-11-02 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Isolation and characterization of new homing endonuclease specificities at individual target site positions.
J.Mol.Biol., 342, 2004
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1U3E
 | | DNA binding and cleavage by the HNH homing endonuclease I-HmuI | | Descriptor: | 1,2-ETHANEDIOL, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 36-MER, ... | | Authors: | Shen, B.W, Landthaler, M, Shub, D.A, Stoddard, B.L. | | Deposit date: | 2004-07-21 | | Release date: | 2004-08-31 | | Last modified: | 2024-04-03 | | Method: | X-RAY DIFFRACTION (2.92 Å) | | Cite: | DNA Binding and Cleavage by the HNH Homing Endonuclease I-HmuI.
J.Mol.Biol., 342, 2004
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7UNJ
 | | De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester matching geometry of purple bacterial special pair, SP1-ZnPPaM | | Descriptor: | 1,2-ETHANEDIOL, SP1-ZnPPaM designed chlorophyll dimer protein, SULFATE ION, ... | | Authors: | Kennedy, M.A, Stoddard, B.L, Ennist, N.M. | | Deposit date: | 2022-04-11 | | Release date: | 2023-04-19 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
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7UNH
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7UNI
 | | De novo designed chlorophyll dimer protein with Zn pheophorbide a methyl ester, SP2-ZnPPaM | | Descriptor: | 1,2-ETHANEDIOL, PHOSPHATE ION, SP2-ZnPPaM designed chlorophyll dimer protein, ... | | Authors: | Kennedy, M.A, Stoddard, B.L, Ennist, N.M. | | Deposit date: | 2022-04-11 | | Release date: | 2023-04-19 | | Last modified: | 2024-06-12 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | De novo design of proteins housing excitonically coupled chlorophyll special pairs.
Nat.Chem.Biol., 2024
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1UJZ
 | | Crystal structure of the E7_C/Im7_C complex; a computationally designed interface between the colicin E7 DNase and the Im7 Immunity protein | | Descriptor: | Designed Colicin E7 DNase, Designed Colicin E7 immunity protein | | Authors: | Kortemme, T, Joachimiak, L.A, Bullock, A.N, Schuler, A.D, Stoddard, B.L, Baker, D. | | Deposit date: | 2003-08-13 | | Release date: | 2004-04-06 | | Last modified: | 2023-10-25 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Computational redesign of protein-protein interaction specificity
NAT.STRUCT.MOL.BIOL., 11, 2004
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1IPP
 | | HOMING ENDONUCLEASE/DNA COMPLEX | | Descriptor: | CADMIUM ION, DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*AP*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON-ENCODED ENDONUCLEASE I-PPOI, ... | | Authors: | Flick, K.E, Jurica, M.S, Monnat Jr, R.J, Stoddard, B.L. | | Deposit date: | 1998-03-19 | | Release date: | 1998-09-02 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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6XR2
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6XR1
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1A73
 | | INTRON-ENCODED ENDONUCLEASE I-PPOI COMPLEXED WITH DNA | | Descriptor: | DNA (5'-D(*TP*TP*GP*AP*CP*TP*CP*TP*CP*TP*TP*AP*A)-3'), DNA (5'-D(P*GP*AP*GP*AP*GP*TP*CP*A)-3'), INTRON 3 (I-PPO) ENCODED ENDONUCLEASE, ... | | Authors: | Flick, K.E, Monnat Junior, R.J, Stoddard, B.L. | | Deposit date: | 1998-03-19 | | Release date: | 1998-10-14 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI.
Nature, 394, 1998
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8TAC
 | | Designed DNA binding protein | | Descriptor: | DBP48, DNA (5'-D(*AP*CP*CP*TP*GP*AP*CP*GP*CP*GP*A)-3'), DNA (5'-D(*TP*TP*CP*GP*CP*GP*TP*CP*AP*GP*GP)-3') | | Authors: | Doyle, L, Stoddard, B.L, Glasscock, C.J, McHugh, R.P, Pecoraro, R.J. | | Deposit date: | 2023-06-27 | | Release date: | 2024-08-28 | | Method: | X-RAY DIFFRACTION (2.34 Å) | | Cite: | Designed DNA binding protein
To Be Published
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8TLP
 | | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x without peptide | | Descriptor: | D_3_633_8x, no peptide, SULFATE ION | | Authors: | Kennedy, M.A, Stoddard, B.L, Hicks, D.R. | | Deposit date: | 2023-07-27 | | Release date: | 2024-12-11 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x, no peptide
To Be Published
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8TM9
 | | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide | | Descriptor: | D_3_633_8x peptide bound, MC1, N-PROPANOL, ... | | Authors: | Kennedy, M.A, Stoddard, B.L, Hicks, D.R. | | Deposit date: | 2023-07-28 | | Release date: | 2024-12-11 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Computationally designed tunable C2 symmetric tandem repeat homodimer, D_3_633_8x bound to peptide
To Be Published
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3U0S
 | | Crystal Structure of an Enzyme Redesigned Through Multiplayer Online Gaming: CE6 | | Descriptor: | 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, Diisopropyl-fluorophosphatase, GLYCEROL, ... | | Authors: | Bale, J.B, Shen, B.W, Stoddard, B.L. | | Deposit date: | 2011-09-29 | | Release date: | 2012-02-01 | | Last modified: | 2024-02-28 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.
Nat.Biotechnol., 30, 2012
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7LVV
 | | cryoEM structure DrdV-DNA complex | | Descriptor: | CALCIUM ION, DNA (27-MER), DNA (28-MER), ... | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2021-02-26 | | Release date: | 2021-03-17 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (3.25 Å) | | Cite: | Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.
Structure, 29, 2021
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7LO5
 | | cryoEM structure DrdV-DNA complex | | Descriptor: | CALCIUM ION, DNA (27-MER), DNA (28-MER), ... | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2021-02-09 | | Release date: | 2021-03-17 | | Last modified: | 2024-03-06 | | Method: | ELECTRON MICROSCOPY (2.86 Å) | | Cite: | Coordination of phage genome degradation versus host genome protection by a bifunctional restriction-modification enzyme visualized by CryoEM.
Structure, 29, 2021
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8W0P
 | | BsaXI -- Type IIB R-M system | | Descriptor: | RM.BsaXI, S-ADENOSYLMETHIONINE, S.BsaXI | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2024-02-13 | | Release date: | 2024-10-30 | | Last modified: | 2025-05-21 | | Method: | ELECTRON MICROSCOPY (3.26 Å) | | Cite: | Atomic insights into the mechanism of DNA recognition and methylation by type IIB restriction-modification system: CryoEM structures of DNA free and cognate DNA bound BsaXI.
To Be Published
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8VX7
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4YXZ
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4YY2
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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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1YSD
 | | Yeast Cytosine Deaminase Double 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 (1.9 Å) | | Cite: | Computational thermostabilization of an enzyme.
Science, 308, 2005
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4YXY
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4YY5
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8W2P
 | | BsaXI-DNA complex I | | Descriptor: | CALCIUM ION, DNA (41-MER) Complementary strand of BsaXI DNA substrate, DNA (41-MER) Top strand of BsaXI cognate DNA substrate, ... | | Authors: | Shen, B.W, Stoddard, B.L, Xu, S. | | Deposit date: | 2024-02-20 | | Release date: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (3.14 Å) | | Cite: | Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI
To Be Published
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