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6UWH
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BU of 6uwh by Molmil
Intermediate engineered variant of I-OnuI meganuclease with improved thermostability and partially altered specificity
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DNA (26-MER), ...
Authors:Werther, R, Stoddard, B.L.
Deposit date:2019-11-05
Release date:2019-12-18
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.299 Å)
Cite:Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.
Structure, 28, 2020
6UWG
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BU of 6uwg by Molmil
Engineered variant of I-OnuI meganuclease with improved thermostability and E178D mutation at catalytic site
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DNA (26-MER), ...
Authors:Werther, R, Stoddard, B.L.
Deposit date:2019-11-05
Release date:2019-12-18
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.22 Å)
Cite:Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.
Structure, 28, 2020
6UW0
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BU of 6uw0 by Molmil
Engineered variant of I-OnuI meganuclease with improved thermostability and fully altered specificity targeting cholera toxin A subunit
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DNA (27-MER), ...
Authors:Werther, R, Stoddard, B.L.
Deposit date:2019-11-04
Release date:2019-12-18
Last modified:2023-10-11
Method:X-RAY DIFFRACTION (2.72 Å)
Cite:Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition.
Structure, 28, 2020
5THG
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BU of 5thg by Molmil
Engineered variant of I-OnuI meganuclease targeting the HIV CCR5 gene; harbors 43 point mutations relative to wild-type I-OnuI
Descriptor: CALCIUM ION, DNA (29-MER), GLYCEROL, ...
Authors:Hallinan, J.P, Stoddard, B.L.
Deposit date:2016-09-29
Release date:2017-05-03
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (3.106 Å)
Cite:The structural basis of altered gene specificity resulting from meganuclease and MegaTAL engineering
to be published
5TGQ
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BU of 5tgq by Molmil
Restriction-modification system Type II R.SwaI, DNA free
Descriptor: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, CALCIUM ION, ...
Authors:Shen, B.W, stoddard, B.L.
Deposit date:2016-09-28
Release date:2016-12-21
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Nucleic Acids Res., 45, 2017
5TGX
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BU of 5tgx by Molmil
Restriction/modification system-Type II R-SwaI complexed with partially cleaved DNA
Descriptor: 1,2-ETHANEDIOL, ACETATE ION, CALCIUM ION, ...
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2016-09-28
Release date:2016-12-21
Last modified:2019-12-25
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target.
Nucleic Acids Res., 45, 2017
1P6O
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BU of 1p6o by Molmil
The crystal structure of yeast cytosine deaminase bound to 4(R)-hydroxyl-3,4-dihydropyrimidine at 1.14 angstroms.
Descriptor: 4-HYDROXY-3,4-DIHYDRO-1H-PYRIMIDIN-2-ONE, ACETIC ACID, CALCIUM ION, ...
Authors:Ireton, G.C, Black, M.E, Stoddard, B.L.
Deposit date:2003-04-29
Release date:2003-08-19
Last modified:2023-08-16
Method:X-RAY DIFFRACTION (1.14 Å)
Cite:The 1.14 a crystal structure of yeast Cytosine deaminase. Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
Structure, 11, 2003
5ESP
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BU of 5esp by Molmil
Crystal Structure of LAGLIDADG Meganuclease I-PanMI with coordinated Calcium ions
Descriptor: CALCIUM ION, DNA (27-MER), GLYCEROL, ...
Authors:Hallinan, J.P, Stoddard, B.L.
Deposit date:2015-11-16
Release date:2016-03-30
Last modified:2024-03-13
Method:X-RAY DIFFRACTION (2.995 Å)
Cite:Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Structure, 24, 2016
5BYO
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BU of 5byo by Molmil
Computationally designed left-handed alpha/alpha toroid with 12 repeats
Descriptor: dTor_12x31L
Authors:Doyle, L, Stoddard, B.L, Bradley, P.
Deposit date:2015-06-10
Release date:2015-12-16
Last modified:2024-03-06
Method:X-RAY DIFFRACTION (2.503 Å)
Cite:Rational design of alpha-helical tandem repeat proteins with closed architectures.
Nature, 528, 2015
1QYS
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BU of 1qys by Molmil
Crystal structure of Top7: A computationally designed protein with a novel fold
Descriptor: TOP7
Authors:Kuhlman, B, Dantas, G, Ireton, G.C, Varani, G, Stoddard, B.L, Baker, D.
Deposit date:2003-09-11
Release date:2003-11-25
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
Science, 302, 2003
1OX7
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BU of 1ox7 by Molmil
Crystal structure of yeast cytosine deaminase apo-enzyme: inorganic zinc bound
Descriptor: CALCIUM ION, Cytosine deaminase, ZINC ION
Authors:Ireton, G.C, Black, M.E, Stoddard, B.L.
Deposit date:2003-04-01
Release date:2003-08-19
Last modified:2011-07-13
Method:X-RAY DIFFRACTION (1.43 Å)
Cite:The 1.14 a crystal structure of yeast Cytosine deaminase. Evolution of nucleotide salvage enzymes and implications for genetic chemotherapy.
Structure, 11, 2003
1Q33
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BU of 1q33 by Molmil
Crystal structure of human ADP-ribose pyrophosphatase NUDT9
Descriptor: ADP-ribose pyrophosphatase, SULFATE ION, beta-D-glucopyranose
Authors:Shen, B.W, Perraud, A.L, Scharenberg, A, Stoddard, B.L.
Deposit date:2003-07-28
Release date:2003-09-30
Last modified:2020-07-29
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:The Crystal Structure and Mutational Analysis of Human NUDT9
J.Mol.Biol., 332, 2003
1R9Y
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BU of 1r9y by Molmil
Bacterial cytosine deaminase D314A mutant.
Descriptor: Cytosine deaminase, FE (III) ION, GLYCEROL, ...
Authors:Mahan, S.D, Ireton, G.C, Stoddard, B.L, Black, M.E.
Deposit date:2003-10-31
Release date:2004-10-05
Last modified:2023-08-23
Method:X-RAY DIFFRACTION (1.57 Å)
Cite:Random mutagenesis and selection of Escherichia coli cytosine deaminase for cancer gene therapy.
Protein Eng.Des.Sel., 17, 2004
1RB7
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BU of 1rb7 by Molmil
Yeast cytosine deaminase crystal form p212121 with sodium acetate.
Descriptor: Cytosine deaminase, ZINC ION
Authors:Ireton, G.C, Stoddard, B.L.
Deposit date:2003-11-02
Release date:2004-03-02
Last modified:2023-08-23
Method:X-RAY DIFFRACTION (2.1 Å)
Cite:Microseed matrix screening to improve crystals of yeast cytosine deaminase.
Acta Crystallogr.,Sect.D, 60, 2004
7RDR
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BU of 7rdr by Molmil
Circular tandem repeat protein with novel repeat topology and enhanced subunit contact surfaces
Descriptor: Circular tendon repeat protein
Authors:Shen, B.W, Stoddard, B.L.
Deposit date:2021-07-10
Release date:2021-09-01
Last modified:2021-11-17
Method:ELECTRON MICROSCOPY (6.5 Å)
Cite:Design of functionalised circular tandem repeat proteins with longer repeat topologies and enhanced subunit contact surfaces.
Commun Biol, 4, 2021
7R9G
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BU of 7r9g by Molmil
Catalytically inactive yeast Pseudouridine Synthase, PUS1, bound to RNA
Descriptor: CHLORIDE ION, RNA (5'-R(*AP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3'), SULFATE ION, ...
Authors:Doyle, L.A, Stoddard, B.L.
Deposit date:2021-06-29
Release date:2021-12-15
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.4 Å)
Cite:The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.
Plos One, 18, 2023
7R9F
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BU of 7r9f by Molmil
Wild-type yeast Pseudouridine Synthase, PUS1, bound to 5-Fluorouracil RNA
Descriptor: RNA (5'-R(*UP*AP*AP*UP*CP*GP*GP*GP*AP*UP*UP*CP*CP*GP*GP*AP*UP*A)-3'), SULFATE ION, tRNA pseudouridine synthase 1
Authors:Doyle, L.A, Stoddard, B.L.
Deposit date:2021-06-29
Release date:2021-12-15
Last modified:2023-11-15
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:The structural basis of mRNA recognition and binding by yeast pseudouridine synthase PUS1.
Plos One, 18, 2023
7RCD
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BU of 7rcd by Molmil
Second stage reengineered variant of I-OnuI targeting human PD1 gene with activity enhancing substitutions
Descriptor: CALCIUM ION, DNA (26-MER), I-OnuI_e-hPD1-c
Authors:Ubilla-Rodriguez, N.C, Werther, R.A, Stoddard, B.L.
Deposit date:2021-07-07
Release date:2022-06-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.448 Å)
Cite:Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
To Be Published
7RCF
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BU of 7rcf by Molmil
Fourth stage reengineered variant of I-OnuI with stability enhancing substitutions
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, CHLORIDE ION, ...
Authors:Ubilla-Rodriguez, N.C, Werther, R.A, Stoddard, B.L.
Deposit date:2021-07-07
Release date:2022-06-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.233 Å)
Cite:Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
To Be Published
7RCE
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BU of 7rce by Molmil
Third stage reengineered variant of I-OnuI with specificity enhancing substitutions
Descriptor: CALCIUM ION, DNA (26-MER), I-OnuI_e-hPD1-d, ...
Authors:Ubilla-Rodriguez, N.C, Werther, R.A, Stoddard, B.L.
Deposit date:2021-07-07
Release date:2022-06-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.42 Å)
Cite:Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
To Be Published
7RCG
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BU of 7rcg by Molmil
I-OnuI_e-hPD1-f final stage reengineered variant of I-OnuI
Descriptor: CALCIUM ION, CHLORIDE ION, DNA (26-MER), ...
Authors:Smiley, A.T, Werther, R.A, Stoddard, B.L.
Deposit date:2021-07-07
Release date:2022-06-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.368 Å)
Cite:Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
To Be Published
7RCC
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BU of 7rcc by Molmil
First stage engineered variant of I-OnuI after initial reassembly
Descriptor: CALCIUM ION, DNA (26-MER), I-OnuI_e-hPD1-b
Authors:Ubilla-Rodriguez, N.C, Werther, R.A, Stoddard, B.L.
Deposit date:2021-07-07
Release date:2022-06-29
Last modified:2023-10-18
Method:X-RAY DIFFRACTION (2.45 Å)
Cite:Characterization of the stepwise engineering and optimization of a retargeted DNA binding protein and gene-editing meganuclease
To Be Published
1IDE
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BU of 1ide by Molmil
ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION)
Descriptor: ISOCITRATE DEHYDROGENASE, ISOCITRIC ACID, MAGNESIUM ION, ...
Authors:Bolduc, J.M, Dyer, D.H, Scott, W.G, Singer, P, Sweet, R.M, Koshland Junior, D.E, Stoddard, B.L.
Deposit date:1995-01-18
Release date:1996-03-08
Last modified:2024-02-07
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.
Science, 268, 1995
4YIS
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BU of 4yis by Molmil
Crystal Structure of LAGLIDADG Meganuclease I-CpaMI Bound to Uncleaved DNA
Descriptor: 1,2-ETHANEDIOL, CALCIUM ION, DNA (28-MER), ...
Authors:Hallinan, J.P, Kaiser, B.K, Stoddard, B.L.
Deposit date:2015-03-02
Release date:2016-03-23
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (2.89 Å)
Cite:Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Structure, 24, 2016
4YHX
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BU of 4yhx by Molmil
Crystal Structure of LAGLIDADG Meganuclease I-GpeMI Bound to Uncleaved DNA
Descriptor: CALCIUM ION, DNA (27-MER), Ribosomal protein 3/homing endonuclease-like fusion protein
Authors:Hallinan, J.P, Kaiser, B.K, Stoddard, B.L.
Deposit date:2015-02-27
Release date:2016-03-09
Last modified:2023-09-27
Method:X-RAY DIFFRACTION (2.15 Å)
Cite:Indirect DNA Sequence Recognition and Its Impact on Nuclease Cleavage Activity.
Structure, 24, 2016

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