1WNR
 
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1V9M
 | | Crystal structure of the C subunit of V-type ATPase from Thermus thermophilus | | Descriptor: | GLYCEROL, V-type ATP synthase subunit C | | Authors: | Numoto, N, Kita, A, Miki, K, RIKEN Structural Genomics/Proteomics Initiative (RSGI) | | Deposit date: | 2004-01-26 | | Release date: | 2004-05-04 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Structure of the C subunit of V-type ATPase from Thermus thermophilus at 1.85 A resolution.
Acta Crystallogr.,Sect.D, 60, 2004
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7VLD
 | | Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLE
 | | Oxy-deoxy intermediate of V2 hemoglobin at 55% oxygen saturation | | Descriptor: | Extracellular A1 globin, Extracellular A2 globin, Extracellular B1 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLF
 | | Oxy-deoxy intermediate of V2 hemoglobin at 26% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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7VLC
 | | Oxy-deoxy intermediate of V2 hemoglobin at 78% oxygen saturation | | Descriptor: | CALCIUM ION, Extracellular A1 globin, Extracellular A2 globin, ... | | Authors: | Numoto, N, Onoda, S, Kawano, Y, Okumura, H, Baba, S, Fukumori, Y, Miki, K, Ito, N. | | Deposit date: | 2021-10-02 | | Release date: | 2022-05-18 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Biophys Physicobio., 19, 2022
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2D2N
 | | Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi | | Descriptor: | Giant hemoglobin, A1(b) globin chain, A2(a5) globin chain, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2005-09-12 | | Release date: | 2005-10-25 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (3.2 Å) | | Cite: | Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Proc.Natl.Acad.Sci.USA, 102, 2005
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2D2M
 | | Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi | | Descriptor: | Giant hemoglobin, A1(b) globin chain, A2(a5) globin chain, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2005-09-12 | | Release date: | 2005-10-25 | | Last modified: | 2024-10-09 | | Method: | X-RAY DIFFRACTION (2.85 Å) | | Cite: | Structure of an extracellular giant hemoglobin of the gutless beard worm Oligobrachia mashikoi.
Proc.Natl.Acad.Sci.USA, 102, 2005
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2ZFO
 | | Structure of the partially unliganded met state of 400 kDa hemoglobin: Insights into ligand-induced structural changes of giant hemoglobins | | Descriptor: | Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, Extracellular giant hemoglobin major globin subunit B1, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-01-08 | | Release date: | 2008-04-22 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins
Proteins, 73, 2008
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3WCU
 | | The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Deoxygenated form | | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | | Deposit date: | 2013-06-01 | | Release date: | 2014-06-04 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
Acta Crystallogr.,Sect.D, 70, 2014
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3WCV
 | | The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: CA bound form | | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | | Deposit date: | 2013-06-01 | | Release date: | 2014-06-04 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
Acta Crystallogr.,Sect.D, 70, 2014
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3WCW
 | | The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: MG bound form | | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | | Deposit date: | 2013-06-01 | | Release date: | 2014-06-04 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
Acta Crystallogr.,Sect.D, 70, 2014
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5ZNO
 | | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S/ mutant in Ca(2+)-bound state | | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL | | Authors: | Numoto, N, Inaba, S, Yamagami, Y, Kamiya, N, Bekker, G.J, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | | Deposit date: | 2018-04-10 | | Release date: | 2018-09-12 | | Last modified: | 2024-11-20 | | Method: | X-RAY DIFFRACTION (1.60264349 Å) | | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry, 57, 2018
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5ZRS
 | | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl adipate bound state | | Descriptor: | 6-ethoxy-6-oxohexanoic acid, Alpha/beta hydrolase family protein, CALCIUM ION, ... | | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | | Deposit date: | 2018-04-25 | | Release date: | 2018-09-12 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.4 Å) | | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry, 57, 2018
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5ZRR
 | | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in monoethyl succinate bound state | | Descriptor: | 4-ethoxy-4-oxobutanoic acid, Alpha/beta hydrolase family protein, GLYCEROL, ... | | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | | Deposit date: | 2018-04-25 | | Release date: | 2018-09-12 | | Last modified: | 2024-11-13 | | Method: | X-RAY DIFFRACTION (1.34 Å) | | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry, 57, 2018
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5ZRQ
 | | Crystal structure of PET-degrading cutinase Cut190 S176A/S226P/R228S mutant in Zn(2+)-bound state | | Descriptor: | Alpha/beta hydrolase family protein, CALCIUM ION, GLYCEROL, ... | | Authors: | Numoto, N, Kamiya, N, Bekker, G.J, Yamagami, Y, Inaba, S, Ishii, K, Uchiyama, S, Kawai, F, Ito, N, Oda, M. | | Deposit date: | 2018-04-25 | | Release date: | 2018-09-12 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.12 Å) | | Cite: | Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle.
Biochemistry, 57, 2018
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3WCT
 | | The structure of a deoxygenated 400 kda hemoglobin provides a more accurate description of the cooperative mechanism of giant hemoglobins: Oxygenated form | | Descriptor: | A1 globin chain of giant V2 hemoglobin, A2 globin chain of giant V2 hemoglobin, B1 globin chain of giant V2 hemoglobin, ... | | Authors: | Numoto, N, Nakagawa, T, Ohara, R, Hasegawa, T, Kita, A, Yoshida, T, Maruyama, T, Imai, K, Fukumori, Y, Miki, K. | | Deposit date: | 2013-06-01 | | Release date: | 2014-06-04 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins
Acta Crystallogr.,Sect.D, 70, 2014
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3A5C
 | | Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, V-type ATP synthase alpha chain, V-type ATP synthase beta chain, ... | | Authors: | Numoto, N, Hasegawa, Y, Takeda, K, Miki, K. | | Deposit date: | 2009-08-06 | | Release date: | 2009-10-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (4.51 Å) | | Cite: | Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
Embo Rep., 10, 2009
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3A5D
 | | Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase | | Descriptor: | V-type ATP synthase alpha chain, V-type ATP synthase beta chain, V-type ATP synthase subunit D, ... | | Authors: | Numoto, N, Hasegawa, Y, Takeda, K, Miki, K. | | Deposit date: | 2009-08-06 | | Release date: | 2009-10-13 | | Last modified: | 2023-11-01 | | Method: | X-RAY DIFFRACTION (4.8 Å) | | Cite: | Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase
Embo Rep., 10, 2009
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2ZS1
 | | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin | | Descriptor: | CHLORIDE ION, Extracellular giant hemoglobin major globin subunit A1, Extracellular giant hemoglobin major globin subunit A2, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-09-02 | | Release date: | 2008-10-21 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Biochemistry, 47, 2008
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2ZS0
 | | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin | | Descriptor: | CALCIUM ION, CHLORIDE ION, Extracellular giant hemoglobin major globin subunit A1, ... | | Authors: | Numoto, N, Nakagawa, T, Kita, A, Sasayama, Y, Fukumori, Y, Miki, K. | | Deposit date: | 2008-09-02 | | Release date: | 2008-10-21 | | Last modified: | 2024-10-30 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Structural Basis for the Heterotropic and Homotropic Interactions of Invertebrate Giant Hemoglobin
Biochemistry, 47, 2008
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8Z2J
 | | Substrate analog a012 bound form of PET-degrading cutinase mutant Cut190**SS_S176A | | Descriptor: | (4-methoxycarbonylphenyl)-(2-phenylmethoxyethoxy)phosphinic acid, (4S)-2-METHYL-2,4-PENTANEDIOL, ACETATE ION, ... | | Authors: | Numoto, N, Kondo, F, Bekker, G.J, Liao, Z, Yamashita, M, Iida, A, Ito, N, Kamiya, N, Oda, M. | | Deposit date: | 2024-04-12 | | Release date: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.89 Å) | | Cite: | Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Int.J.Biol.Macromol., 281, 2024
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8Z2G
 | | MHET bound form of PET-degrading cutinase mutant Cut190*SS_S176A | | Descriptor: | 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, 4-(2-hydroxyethyloxycarbonyl)benzoic acid, AMMONIUM ION, ... | | Authors: | Numoto, N, Kondo, F, Bekker, G.J, Liao, Z, Yamashita, M, Iida, A, Ito, N, Kamiya, N, Oda, M. | | Deposit date: | 2024-04-12 | | Release date: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Int.J.Biol.Macromol., 281, 2024
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8Z2I
 | | Substrate analog a011 bound form of PET-degrading cutinase mutant Cut190**SS_S176A | | Descriptor: | 2-hydroxyethyloxy-(4-methoxycarbonylphenyl)phosphinic acid, Alpha/beta hydrolase family protein, CALCIUM ION | | Authors: | Numoto, N, Kondo, F, Bekker, G.J, Liao, Z, Yamashita, M, Iida, A, Ito, N, Kamiya, N, Oda, M. | | Deposit date: | 2024-04-12 | | Release date: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.38 Å) | | Cite: | Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Int.J.Biol.Macromol., 281, 2024
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8Z2H
 | | Substrate analog a010 bound form of PET-degrading cutinase mutant Cut190**SS_S176A | | Descriptor: | 4-[2-hydroxyethyloxy(oxidanyl)phosphoryl]benzoic acid, Alpha/beta hydrolase family protein, CALCIUM ION | | Authors: | Numoto, N, Kondo, F, Bekker, G.J, Liao, Z, Yamashita, M, Iida, A, Ito, N, Kamiya, N, Oda, M. | | Deposit date: | 2024-04-12 | | Release date: | 2024-11-06 | | Method: | X-RAY DIFFRACTION (1.8 Å) | | Cite: | Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Int.J.Biol.Macromol., 281, 2024
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