7YX7
 
 | | Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 1 spermine molecule at 1.72 A resolution | | Descriptor: | Oligopeptidase B, SPERMINE | | Authors: | Petrenko, D.E, Boyko, K.M, Nikolaeva, A.Y, Vlaskina, A.V, Mikhailova, A.G, Timofeev, V.I, Rakitina, T.V. | | Deposit date: | 2022-02-15 | | Release date: | 2023-01-18 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.72 Å) | | Cite: | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation
Crystals, 12, 2022
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7YWZ
 | | Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution | | Descriptor: | GLYCEROL, Oligopeptidase B, SPERMINE | | Authors: | Petrenko, D.E, Boyko, K.M, Nikolaeva, A.Y, Vlaskina, A.V, Mikhailova, A.G, Timofeev, V.I, Rakitina, T.V. | | Deposit date: | 2022-02-15 | | Release date: | 2023-02-22 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (1.75 Å) | | Cite: | Modified oligopeptidase B from S. proteomaculans in intermediate conformation with 4 spermine molecules at 1.75 A resolution
To Be Published
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7YWP
 | | Closed conformation of Oligopeptidase B from Serratia proteomaculans with covalently bound TCK | | Descriptor: | N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide, Oligopeptidase B | | Authors: | Petrenko, D.E, Boyko, K.M, Nikolaeva, A.Y, Vlaskina, A.V, Mikhailova, A.G, Timofeev, V.I, Rakitina, T.V. | | Deposit date: | 2022-02-14 | | Release date: | 2023-02-22 | | Last modified: | 2024-02-07 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Crystal Structure of Inhibitor-Bound Bacterial Oligopeptidase B in the Closed State: Similarity and Difference between Protozoan and Bacterial Enzymes.
Int J Mol Sci, 24, 2023
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7ZJZ
 | | catalytically non active S532A mutant of oligopeptidase B from S. proteomaculans | | Descriptor: | Oligopeptidase B, SPERMINE | | Authors: | Petrenko, D.E, Boyko, K.M, Nikolaeva, A.Y, Vlaskina, A.V, Mikhailova, A.G, Timofeev, V.I, Rakitina, T.V. | | Deposit date: | 2022-04-12 | | Release date: | 2023-01-18 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation
Crystals, 12, 2022
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8PNW
 | | Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens in holo form with PLP | | Descriptor: | Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase, CHLORIDE ION, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Matyuta, I.O, Boyko, K.M, Nikolaeva, A.Y, Shilova, S.A, Popov, V.O. | | Deposit date: | 2023-07-03 | | Release date: | 2023-10-25 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.
Int J Mol Sci, 24, 2023
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8PNY
 | | Crystal structure of D-amino acid aminotransferase from Blastococcus saxobsidens complexed with phenylhydrazine and in its apo form | | Descriptor: | Branched-chain amino acid aminotransferase/4-amino-4-deoxychorismate lyase, [6-methyl-5-oxidanyl-4-[(2-phenylhydrazinyl)methyl]pyridin-3-yl]methyl dihydrogen phosphate | | Authors: | Matyuta, I.O, Boyko, K.M, Nikolaeva, A.Y, Shilova, S.A, Popov, V.O. | | Deposit date: | 2023-07-03 | | Release date: | 2023-10-25 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Expanded Substrate Specificity in D-Amino Acid Transaminases: A Case Study of Transaminase from Blastococcus saxobsidens.
Int J Mol Sci, 24, 2023
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6UWE
 | | Crystal structure of recombinant thiocyanate dehydrogenase from Thioalkalivibrio paradoxus saturated with copper | | Descriptor: | COPPER (II) ION, UNKNOWN ATOM OR ION, thiocyanate dehydrogenase | | Authors: | Shabalin, I.G, Osipov, E, Tikhonova, T.V, Rakitina, T.V, Boyko, K.M, Popov, V.O. | | Deposit date: | 2019-11-05 | | Release date: | 2019-11-27 | | Last modified: | 2023-10-11 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase.
Proc.Natl.Acad.Sci.USA, 117, 2020
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8YOU
 | | The pmTcDH complex structure with an inhibitor SeCN | | Descriptor: | COPPER (II) ION, GLYCEROL, SELENIUM ATOM, ... | | Authors: | Varfolomeeva, L.A, Polyakov, K.M, Shipkov, N.S, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-13 | | Release date: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The pmTcDH complex structure with an inhibitor SeCN
To Be Published
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8Q9X
 | | The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum with molecular oxygen at 1.05 A resolution | | Descriptor: | COPPER (II) ION, GLYCEROL, OXYGEN MOLECULE, ... | | Authors: | Varfolomeeva, L.A, Polyakov, K.M, Shipkov, N.S, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2023-08-22 | | Release date: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.05 Å) | | Cite: | Structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum at atomic resolution
To Be Published
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8Q9Y
 | | The structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum in complex with inhibitor thiourea at 1.10 A resolution | | Descriptor: | COPPER (II) ION, GLYCEROL, THIOUREA, ... | | Authors: | Varfolomeeva, L.A, Polyakov, K.M, Shipkov, N.S, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2023-08-22 | | Release date: | 2023-09-13 | | Method: | X-RAY DIFFRACTION (1.1 Å) | | Cite: | Structure of thiocyanate dehydrogenase from Pelomicrobium methylotrophicum at atomic resolution
To Be Published
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8P3L
 | | The structure of thiocyanate dehydrogenase mutant form with Thr 169 replaced by Ala from Thioalkalivibrio paradoxus | | Descriptor: | COPPER (II) ION, SULFATE ION, Twin-arginine translocation signal domain-containing protein | | Authors: | Varfolomeeva, L.A, Polyakov, K.M, Komolov, A.S, Rakitina, T.V, Dergousova, N.I, Dorovatovskii, P.V, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2023-05-18 | | Release date: | 2023-05-31 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals
Crystallography Reports, 2023
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8P3M
 | | The structure of thiocyanate dehydrogenase mutant form with Lys 281 replaced by Ala from Thioalkalivibrio paradoxus | | Descriptor: | BORIC ACID, COPPER (II) ION, SODIUM ION, ... | | Authors: | Varfolomeeva, L.A, Polyakov, K.M, Komolov, A.S, Rakitina, T.V, Dergousova, N.I, Dorovatovskii, P.V, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2023-05-18 | | Release date: | 2023-06-07 | | Last modified: | 2024-01-10 | | Method: | X-RAY DIFFRACTION (2.07 Å) | | Cite: | Improvement of the Diffraction Properties of Thiocyanate Dehydrogenase Crystals
Crystallography Reports, 2023
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3GM6
 | | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate | | Descriptor: | (4R)-2-METHYLPENTANE-2,4-DIOL, (4S)-2-METHYL-2,4-PENTANEDIOL, CALCIUM ION, ... | | Authors: | Trofimov, A.A, Polyakov, K.M, Boyko, K.M, Filimonenkov, A.A, Dorovatovsky, P.V, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2009-03-13 | | Release date: | 2009-08-04 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structure of octaheme cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens in a complex with phosphate
Crystallography Reports, 55, 2010
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3F29
 | | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with sulfite | | Descriptor: | 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, CALCIUM ION, Eight-heme nitrite reductase, ... | | Authors: | Trofimov, A.A, Polyakov, K.M, Boyko, K.M, Slutsky, A, Tikhonova, T.V, Antipov, A.N, Zvyagilskaya, R.A, Popov, A.N, Lamzin, V.S, Bourenkov, G.P, Popov, V.O. | | Deposit date: | 2008-10-29 | | Release date: | 2008-12-09 | | Last modified: | 2023-12-27 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase
To be Published
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3OWM
 | | Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine | | Descriptor: | 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE, 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, CALCIUM ION, ... | | Authors: | Trofimov, A.A, Polyakov, K.M, Boyko, K.M, Tikhonova, T.V, Lamzin, V.S, Bourenkov, G.P, Popov, V.O. | | Deposit date: | 2010-09-20 | | Release date: | 2011-10-26 | | Last modified: | 2023-09-06 | | Method: | X-RAY DIFFRACTION (1.65 Å) | | Cite: | Binding of sulfite by the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase
To be Published
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8ONN
 | | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with 3-aminooxypropionic acid | | Descriptor: | 3-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]oxypropanoic acid, Aminotransferase class IV | | Authors: | Matyuta, I.O, Boyko, K.M, Minyaev, M.E, Shilova, S.A, Bezsudnova, E.Y, Popov, V.O. | | Deposit date: | 2023-04-03 | | Release date: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Biochem.J., 480, 2023
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8ONL
 | | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A | | Descriptor: | Aminotransferase class IV, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Matyuta, I.O, Boyko, K.M, Minyaev, M.E, Shilova, S.A, Bezsudnova, E.Y, Popov, V.O. | | Deposit date: | 2023-04-03 | | Release date: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Biochem.J., 480, 2023
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8ONJ
 | | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant R88L | | Descriptor: | Aminotransferase class IV, DI(HYDROXYETHYL)ETHER, PYRIDOXAL-5'-PHOSPHATE | | Authors: | Matyuta, I.O, Boyko, K.M, Minyaev, M.E, Shilova, S.A, Bezsudnova, E.Y, Popov, V.O. | | Deposit date: | 2023-04-03 | | Release date: | 2023-08-30 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | In search for structural targets for engineering d-amino acid transaminase: modulation of pH optimum and substrate specificity.
Biochem.J., 480, 2023
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8ONM
 | | Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with D-glutamate | | Descriptor: | (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid, 1,2-ETHANEDIOL, 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE, ... | | Authors: | Matyuta, I.O, Boyko, K.M, Minyaev, M.E, Shilova, S.A, Bezsudnova, E.Y, Popov, V.O. | | Deposit date: | 2023-04-03 | | Release date: | 2024-04-10 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Probing of the structural and catalytic roles of the residues in the active site of transaminase from Aminobacterium colombiense
To Be Published
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8QND
 | | Crystal structure of the ribonucleoside hydrolase C from Lactobacillus reuteri | | Descriptor: | CALCIUM ION, Inosine-uridine nucleoside N-ribohydrolase | | Authors: | Matyuta, I.O, Minyaev, M.E, Shaposhnikov, L.A, Pometun, E.V, Tishkov, V.I, Popov, V.O, Boyko, K.M. | | Deposit date: | 2023-09-26 | | Release date: | 2023-12-20 | | Last modified: | 2024-01-24 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structure-Functional Examination of Novel Ribonucleoside Hydrolase C (RihC) from Limosilactobacillus reuteri LR1.
Int J Mol Sci, 25, 2023
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8YTR
 | | The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus | | Descriptor: | COPPER (II) ION, CopC domain-containing protein, DI(HYDROXYETHYL)ETHER | | Authors: | Kulikova, O.G, Solovieva, A.Y, Varfolomeeva, L.A, Dergousova, N.I, Nikolaeva, A.Y, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-26 | | Release date: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | The structure of Cu(II)-CopC from Thioalkalivibrio paradoxus
To Be Published
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8YTS
 | | The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution | | Descriptor: | Cytochrome C, HEME C | | Authors: | Varfolomeeva, L.A, Solovieva, A.Y, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-26 | | Release date: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.15 Å) | | Cite: | The structure of the cytochrome c546/556 from Thioalkalivibrio paradoxus with unusual UV-Vis spectral features at atomic resolution
To Be Published
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8YU6
 | | The structure of thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q), activated by crystal soaking with 1mM CuCl2 and 1 mM sodium ascorbate | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, COPPER (II) ION, ... | | Authors: | Varfolomeeva, L.A, Shipkov, N.S, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-26 | | Release date: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | The structure of thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q), activated by crystal soaking with 1mM CuCl2 and 1 mM sodium ascorbate
To Be Published
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8YTQ
 | | The structure of apoCopC from Thioalkalivibrio paradoxus | | Descriptor: | ACETATE ION, COPPER (II) ION, CopC domain-containing protein, ... | | Authors: | Kulikova, O.G, Solovieva, A.Y, Varfolomeeva, L.A, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-26 | | Release date: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | The structure of apoCopC from Thioalkalivibrio paradoxus
To Be Published
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8YU5
 | | The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q) | | Descriptor: | 1,2-ETHANEDIOL, CHLORIDE ION, COPPER (II) ION, ... | | Authors: | Varfolomeeva, L.A, Shipkov, N.S, Dergousova, N.I, Boyko, K.M, Tikhonova, T.V, Popov, V.O. | | Deposit date: | 2024-03-26 | | Release date: | 2024-04-24 | | Method: | X-RAY DIFFRACTION (1.45 Å) | | Cite: | The structure of non-activated thiocyanate dehydrogenase mutant with the H447Q substitution from Pelomicrobium methylotrophicum (pmTcDH H447Q)
To Be Published
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