4UB6
 
 | | Native structure of photosystem II (dataset-1) by a femtosecond X-ray laser | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | | Deposit date: | 2014-08-12 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
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7BYV
 | | Crystal structure of exo-beta-1,3-galactanase from Phanerochaete chrysosporium Pc1,3Gal43A E208Q with beta-1,3-galactotriose | | Descriptor: | 2-acetamido-2-deoxy-beta-D-glucopyranose, CALCIUM ION, Galactan 1,3-beta-galactosidase, ... | | Authors: | Matsuyama, K, Ishida, T, Kishine, N, Fujimoto, Z, Igarashi, K, Kaneko, S. | | Deposit date: | 2020-04-24 | | Release date: | 2020-11-04 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2.5 Å) | | Cite: | Unique active-site and subsite features in the arabinogalactan-degrading GH43 exo-beta-1,3-galactanase from Phanerochaete chrysosporium .
J.Biol.Chem., 295, 2020
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7BUS
 | | Chalcone synthase from Glycine max (L.) Merr (soybean) | | Descriptor: | Chalcone synthase | | Authors: | Imaizumi, R, Mameda, R, Takeshita, K, Waki, T, Kubo, H, Sakai, N, Nakata, S, Takahashi, S, Kataoka, K, Yamamoto, M, Yamashita, S, Nakayama, T. | | Deposit date: | 2020-04-08 | | Release date: | 2020-08-19 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.52 Å) | | Cite: | Crystal structure of chalcone synthase, a key enzyme for isoflavonoid biosynthesis in soybean.
Proteins, 2020
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4UB8
 | | Native structure of photosystem II (dataset-2) by a femtosecond X-ray laser | | Descriptor: | 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL, 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE, 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE, ... | | Authors: | Suga, M, Akita, F, Hirata, K, Ueno, G, Murakami, H, Nakajima, Y, Shimizu, T, Yamashita, K, Yamamoto, M, Ago, H, Shen, J.R. | | Deposit date: | 2014-08-12 | | Release date: | 2014-12-03 | | Last modified: | 2024-10-23 | | Method: | X-RAY DIFFRACTION (1.95 Å) | | Cite: | Native structure of photosystem II at 1.95 angstrom resolution viewed by femtosecond X-ray pulses.
Nature, 517, 2015
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1H0G
 | | Complex of a chitinase with the natural product cyclopentapeptide argadin from Clonostachys | | Descriptor: | Argadin, CHITINASE B, GLYCEROL | | Authors: | Houston, D, Shiomi, K, Arai, N, Omura, S, Peter, M.G, Turberg, A, Synstad, B, Eijsink, V.G.H, Aalten, D.M.F. | | Deposit date: | 2002-06-19 | | Release date: | 2002-06-27 | | Last modified: | 2023-12-13 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | High Resolution Inhibited Complexes of a Chitinase with Natural Product Cyclopentapeptides - Peptide Mimicry of a Carbohydrate Substrate
Proc.Natl.Acad.Sci.USA, 99, 2002
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7PCE
 | | BurG (apo): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | ADENOSINE-5'-DIPHOSPHATE, Ketol-acid reductoisomerase, PHOSPHATE ION | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.9 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCC
 | | BurG in complex with Mg2+ and NAD+ (holo): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | GLYCEROL, Ketol-acid reductoisomerase, MAGNESIUM ION, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCG
 | | BurG (holo) in complex with cyclopropane-1,1-dicarboxylate (7): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | GLYCEROL, Ketol-acid reductoisomerase, MAGNESIUM ION, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCM
 | | BurG (holo) in complex with (Z)-2,3-dihydroxy-6-methyl-hept-2-enoate (13): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (Z)-6-methyl-2,3-bis(oxidanyl)hept-2-enoic acid, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCO
 | | BurG E232Q mutant (holo) in complex with 2R,3R-2,3-dihydroxy-6-methyl-heptanoate (12): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (2R,3R)-6-methyl-2,3-bis(oxidanyl)heptanoic acid, GLYCEROL, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.55 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCI
 | | BurG (holo) in complex with hydroxypyruvate-enol (8): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (Z)-2,3-bis(oxidanyl)prop-2-enoic acid, IMIDAZOLE, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.9 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCT
 | | BurG E232Q mutant (holo) in complex with enol-oxalacetate (15): Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (~{Z})-2-oxidanylbut-2-enedioic acid, GLYCEROL, Ketol-acid reductoisomerase, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-04 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.35 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCL
 | | BurG (holo) in complex with 2-hydroxy-2-(hydroxy(isopropyl)amino)acetate (11): Biosynthesis of cyclopropanolrings in bacterial toxins | | Descriptor: | (2S)-2-oxidanyl-2-[oxidanyl(propan-2-yl)amino]ethanoic acid, Ketol-acid reductoisomerase, MAGNESIUM ION, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.05 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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7PCN
 | | BurG (holo) in complex with gonyenediol (14), trigonic acid (6) and DMS: Biosynthesis of cyclopropanol rings in bacterial toxins | | Descriptor: | (2R)-2-oxidanyl-2-(1-oxidanylcyclopropyl)ethanoic acid, (METHYLSULFANYL)METHANE, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, ... | | Authors: | Trottmann, F, Ishida, K, Ishida, M, Kries, H, Groll, M, Hertweck, C. | | Deposit date: | 2021-08-03 | | Release date: | 2022-08-10 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (1.6 Å) | | Cite: | Pathogenic bacteria remodel central metabolic enzyme to build a cyclopropanol warhead.
Nat.Chem., 14, 2022
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4U9L
 | | Structure of a membrane protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MAGNESIUM ION, Magnesium transporter MgtE | | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-08-06 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.3 Å) | | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE
Nat Commun, 5, 2014
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4U9N
 | | Structure of a membrane protein | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, MANGANESE (II) ION, Magnesium transporter MgtE, ... | | Authors: | Takeda, H, Hattori, M, Nishizawa, T, Yamashita, K, Shah, S.T.A, Caffrey, M, Maturana, A.D, Ishitani, R, Nureki, O. | | Deposit date: | 2014-08-06 | | Release date: | 2014-12-03 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Structural basis for ion selectivity revealed by high-resolution crystal structure of Mg(2+) channel MgtE
Nat Commun, 5, 2014
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5X1F
 | | CO bound cytochrome c oxidase without pump laser irradiation at 278K | | Descriptor: | (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE, (1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE, (7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE, ... | | Authors: | Shimada, A, Kubo, M, Baba, S, Yamashita, K, Hirata, K, Ueno, G, Nomura, T, Kimura, T, Shinzawa-Itoh, K, Baba, J, Hatano, K, Eto, Y, Miyamoto, A, Murakami, H, Kumasaka, T, Owada, S, Tono, K, Yabashi, M, Yamaguchi, Y, Yanagisawa, S, Sakaguchi, M, Ogura, T, Komiya, R, Yan, J, Yamashita, E, Yamamoto, M, Ago, H, Yoshikawa, S, Tsukihara, T. | | Deposit date: | 2017-01-25 | | Release date: | 2017-08-09 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | A nanosecond time-resolved XFEL analysis of structural changes associated with CO release from cytochrome c oxidase.
Sci Adv, 3, 2017
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5WY1
 | | Crystal structure of mouse DNA methyltransferase 1 (T1505A mutant) | | Descriptor: | DNA (cytosine-5)-methyltransferase 1, ZINC ION | | Authors: | Kanada, K, Takeshita, K, Suetake, I, Tajima, S, Nakagawa, A. | | Deposit date: | 2017-01-10 | | Release date: | 2017-05-24 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (3.27 Å) | | Cite: | Conserved threonine 1505 in the catalytic domain stabilizes mouse DNA methyltransferase 1
J. Biochem., 162, 2017
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9IHS
 | | Microbial transglutaminase mutant - D3C/G283C | | Descriptor: | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, CHLORIDE ION, DI(HYDROXYETHYL)ETHER, ... | | Authors: | Suzuki, M, Date, M, Kashiwagi, T, Takahashi, K, Nakamura, A, Tanokura, M, Suzuki, E, Yokoyama, K. | | Deposit date: | 2024-06-18 | | Release date: | 2024-09-18 | | Last modified: | 2024-10-16 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Random mutagenesis and disulfide bond formation improved thermostability in microbial transglutaminase.
Appl.Microbiol.Biotechnol., 108, 2024
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6L0Q
 | | Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with O-Phosphoserine | | Descriptor: | (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid, (4S)-2-METHYL-2,4-PENTANEDIOL, Protein CysO | | Authors: | Nakabayashi, M, Takeda, E, Ishikawa, K, Nakamura, T. | | Deposit date: | 2019-09-26 | | Release date: | 2020-09-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.58 Å) | | Cite: | Identification of amino acid residues important for recognition of O-phospho-l-serine substrates by cysteine synthase.
J.Biosci.Bioeng., 131, 2021
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6L0P
 | | Crystal Structure of the O-Phosphoserine Sulfhydrylase from Aeropyrum pernix Complexed with O-Phosphoserine | | Descriptor: | (2S)-2-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]-3-phosphonooxy-propanoic acid, (4S)-2-METHYL-2,4-PENTANEDIOL, Protein CysO | | Authors: | Nakabayashi, M, Takeda, E, Ishikawa, K, Nakamura, T. | | Deposit date: | 2019-09-26 | | Release date: | 2020-09-23 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (1.79 Å) | | Cite: | Identification of amino acid residues important for recognition of O-phospho-l-serine substrates by cysteine synthase.
J.Biosci.Bioeng., 131, 2021
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5Y5L
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the absence of NADH (resting state) | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5I
 | | Time-resolved SFX structure of cytochrome P450nor: 20 ms after photo-irradiation of caged NO in the presence of NADH (NO-bound state), light data | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, ... | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5J
 | | Time-resolved SFX structure of cytochrome P450nor: dark-2 data in the presence of NADH (resting state) | | Descriptor: | GLYCEROL, NADP nitrous oxide-forming nitric oxide reductase, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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5Y5K
 | | Time-resolved SFX structure of cytochrome P450nor : 20 ms after photo-irradiation of caged NO in the absence of NADH (NO-bound state), light data | | Descriptor: | NADP nitrous oxide-forming nitric oxide reductase, NITRIC OXIDE, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Tosha, T, Nomura, T, Nishida, T, Saeki, N, Okubayashi, K, Yamagiwa, R, Sugahara, M, Nakane, T, Yamashita, K, Hirata, K, Ueno, G, Kimura, T, Hisano, T, Muramoto, K, Sawai, H, Takeda, H, Mizohata, E, Yamashita, A, Kanematsu, Y, Takano, Y, Nango, E, Tanaka, R, Nureki, O, Ikemoto, Y, Murakami, H, Owada, S, Tono, K, Yabashi, M, Yamamoto, M, Ago, H, Iwata, S, Sugimoto, H, Shiro, Y, Kubo, M. | | Deposit date: | 2017-08-09 | | Release date: | 2017-12-06 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate.
Nat Commun, 8, 2017
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