8W2Q
 
 | | BsaXI-DNA complex II | | Descriptor: | DNA (41-MER), RM.BsaXI, S-ADENOSYL-L-HOMOCYSTEINE, ... | | Authors: | Shen, B.W, Stoddard, B.L, Xu, S. | | Deposit date: | 2024-02-21 | | Release date: | 2024-10-30 | | Method: | ELECTRON MICROSCOPY (3.06 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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5BYO
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299D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: THE HAMMERHEAD RIBOZYME | | Descriptor: | RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-14 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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1QVJ
 | | structure of NUDT9 complexed with ribose-5-phosphate | | Descriptor: | 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 5-O-phosphono-beta-D-ribofuranose, ADP-ribose pyrophosphatase, ... | | Authors: | Shen, B.W, Perraud, A.-L, Scharenberg, A.S, Stoddard, B.L. | | Deposit date: | 2003-08-27 | | Release date: | 2003-09-16 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (1.91 Å) | | Cite: | The crystal structure and mutational analysis of human NUDT9
J.Mol.Biol., 332, 2003
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6UVW
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6UWK
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6UWH
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6UW0
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6UWG
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6UWJ
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301D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMMERHEAD RIBOZYME, MG(II)-SOAKED | | Descriptor: | MAGNESIUM ION, RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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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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5ESP
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300D
 | | CAPTURING THE STRUCTURE OF A CATALYTIC RNA INTERMEDIATE: RNA HAMMERHEAD RIBOZYME, MN(II)-SOAKED | | Descriptor: | MANGANESE (II) ION, RNA HAMMERHEAD RIBOZYME | | Authors: | Scott, W.G, Murray, J.B, Arnold, J.R.P, Stoddard, B.L, Klug, A. | | Deposit date: | 1996-12-14 | | Release date: | 1997-01-24 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (3 Å) | | Cite: | Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme.
Science, 274, 1996
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3BVQ
 | | Crystal Structure of Apo NotI Restriction Endonuclease | | Descriptor: | FE (III) ION, NotI restriction endonuclease, SULFATE ION | | Authors: | Lambert, A.R, Sussman, D, Shen, B, Stoddard, B.L. | | Deposit date: | 2008-01-07 | | Release date: | 2008-01-22 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Structure, 16, 2008
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3C25
 | | Crystal Structure of NotI Restriction Endonuclease Bound to Cognate DNA | | Descriptor: | CALCIUM ION, DNA (5'-D(*DCP*DGP*DGP*DAP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DGP*DCP*DCP*DG)-3'), DNA (5'-D(*DCP*DGP*DGP*DCP*DGP*DGP*DCP*DGP*DCP*DGP*DGP*DCP*DCP*DGP*DCP*DGP*DCP*DCP*DTP*DCP*DCP*DG)-3'), ... | | Authors: | Lambert, A.R, Sussman, D, Shen, B, Stoddard, B.L. | | Deposit date: | 2008-01-24 | | Release date: | 2008-02-12 | | Last modified: | 2024-02-21 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Structures of the Rare-Cutting Restriction Endonuclease NotI Reveal a Unique Metal Binding Fold Involved in DNA Binding.
Structure, 16, 2008
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2EX5
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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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6MAF
 | | native BbvCI A2B2 tetramer at low resolution | | Descriptor: | BbvCI endonuclease subunit 1, BbvCI endonuclease subunit 2 | | Authors: | Shen, B.W, Stoddard, B.L. | | Deposit date: | 2018-08-27 | | Release date: | 2018-11-14 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (3.79 Å) | | Cite: | Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.
Nucleic Acids Res., 47, 2019
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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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1IDE
 | | 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
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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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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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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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7RDR
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