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PDB: 86 results
7DC0
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BU of 7dc0 by Molmil
Crystal structure of glycan-free Pseudomonas taiwanensis lectin
Descriptor: Lectin, SULFATE ION
Authors:Oda, K, Matoba, Y.
Deposit date:2020-10-23
Release date:2021-04-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.88 Å)
Cite:Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.
J.Biol.Chem., 296, 2021
7DC4
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BU of 7dc4 by Molmil
Crystal structure of glycan-bound Pseudomonas taiwanensis lectin
Descriptor: Lectin, SULFATE ION, alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose
Authors:Oda, K, Matoba, Y.
Deposit date:2020-10-23
Release date:2021-04-28
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (0.95 Å)
Cite:Lectins engineered to favor a glycan-binding conformation have enhanced antiviral activity.
J.Biol.Chem., 296, 2021
3VVL
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BU of 3vvl by Molmil
Crystal structure of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway
Descriptor: Homoserine O-acetyltransferase
Authors:Oda, K, Matoba, Y, Kumagai, T, Noda, M, Sugiyama, M.
Deposit date:2012-07-26
Release date:2013-03-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.81 Å)
Cite:Crystallographic study to determine the substrate specificity of an L-serine-acetylating enzyme found in the D-cycloserine biosynthetic pathway
J.Bacteriol., 195, 2013
6LE4
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BU of 6le4 by Molmil
Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with cystathionine
Descriptor: (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid, Cystathionine gamma-lyase, PHOSPHATE ION
Authors:Oda, K, Matoba, Y.
Deposit date:2019-11-24
Release date:2020-10-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (3.1 Å)
Cite:Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis.
Sci Rep, 10, 2020
6LDO
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BU of 6ldo by Molmil
Crystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with L-serine
Descriptor: (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine, Cystathionine gamma-lyase, PHOSPHATE ION
Authors:Oda, K, Matoba, Y.
Deposit date:2019-11-22
Release date:2020-10-07
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.75 Å)
Cite:Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis.
Sci Rep, 10, 2020
6LUH
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BU of 6luh by Molmil
High resolution structure of N(omega)-hydroxy-L-arginine hydrolase
Descriptor: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
Authors:Oda, K, Matoba, Y.
Deposit date:2020-01-28
Release date:2020-09-02
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway.
Acta Crystallogr D Struct Biol, 76, 2020
7C86
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BU of 7c86 by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: Dark state structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, RETINAL, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2020-05-28
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.3 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
8IUS
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BU of 8ius by Molmil
Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with reduced Cys86
Descriptor: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
Authors:Oda, K, Matoba, Y.
Deposit date:2023-03-25
Release date:2024-03-27
Method:X-RAY DIFFRACTION (2.14 Å)
Cite:Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUU
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BU of 8iuu by Molmil
Crystal structure of Manganese-rebound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
Descriptor: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
Authors:Oda, K, Matoba, Y.
Deposit date:2023-03-25
Release date:2024-03-27
Method:X-RAY DIFFRACTION (1.26 Å)
Cite:Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUV
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BU of 8iuv by Molmil
Crystal structure of Manganese-free N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
Descriptor: MAGNESIUM ION, MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
Authors:Oda, K, Matoba, Y.
Deposit date:2023-03-25
Release date:2024-03-27
Method:X-RAY DIFFRACTION (1.75 Å)
Cite:Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUT
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BU of 8iut by Molmil
Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with reduced Cys86
Descriptor: COPPER (I) ION, COPPER (II) ION, MAGNESIUM ION, ...
Authors:Oda, K, Matoba, Y.
Deposit date:2023-03-25
Release date:2024-03-27
Method:X-RAY DIFFRACTION (1.58 Å)
Cite:Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
8IUW
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BU of 8iuw by Molmil
Crystal structure of Copper-bound N(omega)-hydroxy-L-arginine hydrolase with oxidized Cys86
Descriptor: COPPER (I) ION, COPPER (II) ION, MAGNESIUM ION, ...
Authors:Oda, K, Matoba, Y.
Deposit date:2023-03-25
Release date:2024-03-27
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:Copper inactivates DcsB by oxidation of the Cys86 to cysteine sulfinic aicd
To Be Published
7E6Z
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BU of 7e6z by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 50 microsecond structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2021-02-24
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
7E6Y
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BU of 7e6y by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 microsecond structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2021-02-24
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
7E6X
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BU of 7e6x by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 4 ms structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2021-02-24
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
7E70
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BU of 7e70 by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 250 microsecond structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2021-02-24
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
7E71
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BU of 7e71 by Molmil
Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin: 1 ms structure
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Archaeal-type opsin 1,Archaeal-type opsin 2, ...
Authors:Oda, K, Nomura, T, Nakane, T, Yamashita, K, Inoue, K, Ito, S, Vierock, J, Hirata, K, Maturana, A.D, Katayama, K, Ikuta, T, Ishigami, I, Izume, T, Umeda, R, Eguma, R, Oishi, S, Kasuya, G, Kato, T, Kusakizako, T, Shihoya, W, Shimada, H, Takatsuji, T, Takemoto, M, Taniguchi, R, Tomita, A, Nakamura, R, Fukuda, M, Miyauchi, H, Lee, Y, Nango, E, Tanaka, R, Tanaka, T, Sugahara, M, Kimura, T, Shimamura, T, Fujiwara, T, Yamanaka, Y, Owada, S, Joti, Y, Tono, K, Ishitani, R, Hayashi, S, Kandori, H, Hegemann, P, Iwata, S, Kubo, M, Nishizawa, T, Nureki, O.
Deposit date:2021-02-24
Release date:2021-04-07
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (2.5 Å)
Cite:Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin.
Elife, 10, 2021
8WKO
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BU of 8wko by Molmil
Crystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the closed form
Descriptor: (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid, L-methionine gamma-lyase, PROLINE, ...
Authors:Oda, K, Matoba, Y.
Deposit date:2023-09-28
Release date:2024-02-14
Last modified:2024-06-19
Method:X-RAY DIFFRACTION (2.91 Å)
Cite:pH-dependent regulation of an acidophilic O -acetylhomoserine sulfhydrylase from Lactobacillus plantarum.
Appl.Environ.Microbiol., 90, 2024
8WKR
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BU of 8wkr by Molmil
Crystal structure of O-acetylhomoserine sulfhydrylase from Lactobacillus plantarum in the open form
Descriptor: (2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid, L-methionine gamma-lyase, PROLINE
Authors:Oda, K, Matoba, Y.
Deposit date:2023-09-28
Release date:2024-02-14
Last modified:2024-06-19
Method:X-RAY DIFFRACTION (2.05 Å)
Cite:pH-dependent regulation of an acidophilic O -acetylhomoserine sulfhydrylase from Lactobacillus plantarum.
Appl.Environ.Microbiol., 90, 2024
7CCS
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BU of 7ccs by Molmil
Consensus mutated xCT-CD98hc complex
Descriptor: 4F2 cell-surface antigen heavy chain, Consensus mutated Anionic Amino Acid Transporter Light Chain, Xc- System
Authors:Oda, K, Lee, Y, Takemoto, M, Yamashita, K, Nishizawa, T, Nureki, O.
Deposit date:2020-06-17
Release date:2020-12-09
Last modified:2020-12-16
Method:ELECTRON MICROSCOPY (6.2 Å)
Cite:Consensus mutagenesis approach improves the thermal stability of system x c - transporter, xCT, and enables cryo-EM analyses.
Protein Sci., 29, 2020
6LUG
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BU of 6lug by Molmil
Crystal structure of N(omega)-hydroxy-L-arginine hydrolase
Descriptor: MANGANESE (II) ION, N(omega)-hydroxy-L-arginine amidinohydrolase
Authors:Oda, K, Matoba, Y.
Deposit date:2020-01-28
Release date:2020-06-17
Last modified:2024-03-27
Method:X-RAY DIFFRACTION (1.9 Å)
Cite:Crystal structure of an Nomega-hydroxy-L-arginine hydrolase found in the D-cycloserine biosynthetic pathway.
Acta Crystallogr D Struct Biol, 76, 2020
5ZIH
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BU of 5zih by Molmil
Crystal structure of the red light-activated channelrhodopsin Chrimson.
Descriptor: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, Sensory opsin A,Chrimson
Authors:Oda, K, Vierock, J, Oishi, S, Taniguchi, R, Yamashita, K, Nishizawa, T, Hegemann, P, Nureki, O.
Deposit date:2018-03-15
Release date:2018-11-21
Last modified:2023-11-22
Method:X-RAY DIFFRACTION (2.6 Å)
Cite:Crystal structure of the red light-activated channelrhodopsin Chrimson.
Nat Commun, 9, 2018
7CIT
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BU of 7cit by Molmil
Crystal structure of tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h
Descriptor: COPPER (II) ION, HYDROGEN PEROXIDE, MelC, ...
Authors:Oda, K, Matoba, Y.
Deposit date:2020-07-08
Release date:2021-06-16
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.5 Å)
Cite:The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.
Int.J.Biol.Macromol., 183, 2021
7CIY
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BU of 7ciy by Molmil
Crystal structure of N191G-mutated tyrosinase from Streptomyces castaneoglobisporus in complex with the caddie protein obtained by soaking in the solution containing Cu(II) and hydroxylamine for 24 h
Descriptor: COPPER (II) ION, HYDROGEN PEROXIDE, MelC, ...
Authors:Oda, K, Matoba, Y.
Deposit date:2020-07-08
Release date:2021-06-16
Last modified:2023-11-29
Method:X-RAY DIFFRACTION (1.47 Å)
Cite:The basicity of an active-site water molecule discriminates between tyrosinase and catechol oxidase activity.
Int.J.Biol.Macromol., 183, 2021
3VVM
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BU of 3vvm by Molmil
Crystal structure of G52A-P55G mutant of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway
Descriptor: Homoserine O-acetyltransferase
Authors:Oda, K, Matoba, Y, Kumagai, T, Noda, M, Sugiyama, M.
Deposit date:2012-07-26
Release date:2013-03-20
Last modified:2023-11-08
Method:X-RAY DIFFRACTION (1.7 Å)
Cite:Crystallographic study to determine the substrate specificity of an L-serine-acetylating enzyme found in the D-cycloserine biosynthetic pathway
J.Bacteriol., 195, 2013

 

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