8A7V
 
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8AM4
 | | Cl-rsEGFP2 Long Wavelength Structure | | Descriptor: | Green fluorescent protein | | Authors: | Orr, C.M, Fadini, A, van Thor, J. | | Deposit date: | 2022-08-02 | | Release date: | 2023-08-02 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.02 Å) | | Cite: | Serial Femtosecond Crystallography Reveals that Photoactivation in a Fluorescent Protein Proceeds via the Hula Twist Mechanism.
J.Am.Chem.Soc., 2023
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6YRJ
 | | SFX structure of dye-type peroxidase DtpB in the ferric state | | Descriptor: | MAGNESIUM ION, PROTOPORPHYRIN IX CONTAINING FE, Putative iron-dependent peroxidase | | Authors: | Lucic, M, Axford, D.A, Owen, R.L, Worrall, J.A.R, Hough, M.A. | | Deposit date: | 2020-04-20 | | Release date: | 2021-01-13 | | Last modified: | 2024-05-01 | | Method: | X-RAY DIFFRACTION (1.85 Å) | | Cite: | Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe IV =O Formation.
Angew.Chem.Int.Ed.Engl., 59, 2020
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7KCU
 | | Joint neutron/X-ray structure of Oxyferrous Dehaloperoxidase B | | Descriptor: | Dehaloperoxidase B, OXYGEN MOLECULE, PROTOPORPHYRIN IX CONTAINING FE, ... | | Authors: | Carey, L.M, Ghiladi, R.A, Meilleur, F, Myles, D. | | Deposit date: | 2020-10-07 | | Release date: | 2021-10-13 | | Last modified: | 2023-10-25 | | Method: | NEUTRON DIFFRACTION (2.2 Å), X-RAY DIFFRACTION | | Cite: | Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.
Iucrj, 9, 2022
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7JOR
 | | Neutron structure of ferric Dehaloperoxidase B | | Descriptor: | 2-(2-METHOXYETHOXY)ETHANOL, Dehaloperoxidase B, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Carey, L.M, Ghiladi, R.A, Meilleur, F, Myles, D.A.A. | | Deposit date: | 2020-08-07 | | Release date: | 2021-09-08 | | Last modified: | 2024-04-03 | | Method: | NEUTRON DIFFRACTION (2.05 Å) | | Cite: | Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.
Iucrj, 9, 2022
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8K6Y
 | | Serial femtosecond crystallography structure of photo dissociated CO from ba3- type cytochrome c oxidase determined by extrapolation method | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, CARBON MONOXIDE, COPPER (II) ION, ... | | Authors: | Safari, C, Ghosh, S, Andersson, R, Johannesson, J, Donoso, A.V, Zoric, D, Sandelin, E, Iwata, S, Neutze, R, Branden, G. | | Deposit date: | 2023-07-25 | | Release date: | 2023-11-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.
Sci Adv, 9, 2023
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8K65
 | | Serial femtosecond crystallography structure of CO bound ba3- type cytochrome c oxidase without pump laser irradiation | | Descriptor: | (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate, CARBON MONOXIDE, COPPER (II) ION, ... | | Authors: | Safari, C, Ghosh, S, Andersson, R, Johannesson, J, Donoso, A.V, Bath, P, Zoric, D, Sandelin, E, Nango, E, Tanaka, R, Iwata, S, Neutze, R, Branden, G. | | Deposit date: | 2023-07-25 | | Release date: | 2023-11-15 | | Last modified: | 2024-03-20 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase.
Sci Adv, 9, 2023
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5ZLG
 | | Human duodenal cytochrome b (Dcytb) in zinc ion and ascorbate bound form | | Descriptor: | ASCORBIC ACID, Cytochrome b reductase 1, PROTOPORPHYRIN IX CONTAINING FE, ... | | Authors: | Ganasen, M, Togashi, H, Mauk, G.A, Shiro, Y, Sawai, H, Sugimoto, H. | | Deposit date: | 2018-03-27 | | Release date: | 2018-10-31 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.8 Å) | | Cite: | Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate.
Commun Biol, 1, 2018
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5ZLE
 | | Human duodenal cytochrome b (Dcytb) in substrate free form | | Descriptor: | Cytochrome b reductase 1, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Ganasen, M, Togashi, H, Mauk, G.A, Shiro, Y, Sawai, H, Sugimoto, H. | | Deposit date: | 2018-03-27 | | Release date: | 2018-10-31 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate.
Commun Biol, 1, 2018
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5GJ3
 | | Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in two-heme bound form (holo-2) | | Descriptor: | PROTOPORPHYRIN IX CONTAINING FE, Periplasmic binding protein, ZINC ION | | Authors: | Rahman, M.M, Naoe, Y, Nakamura, N, Shiro, Y, Sugimoto, H. | | Deposit date: | 2016-06-26 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (2 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85, 2017
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5GIZ
 | | Periplasmic heme-binding protein BhuT in apo form | | Descriptor: | CHLORIDE ION, Putative hemin transport system, substrate-binding protein, ... | | Authors: | Nakamura, N, Naoe, Y, Rahman, M.M, Shiro, Y, Sugimoto, H. | | Deposit date: | 2016-06-26 | | Release date: | 2017-06-28 | | Last modified: | 2023-11-08 | | Method: | X-RAY DIFFRACTION (1.5 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems.
Proteins, 85, 2017
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7ADQ
 | | Serial Laue crystallography structure of dehaloperoxidase B from Amphitrite ornata | | Descriptor: | Dehaloperoxidase B, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION | | Authors: | Moreno-Chicano, T.M, Ebrahim, A.E, Srajer, V, Henning, R.W, Doak, B.C, Trebbin, M, Monteiro, D.C.F, Hough, M.A. | | Deposit date: | 2020-09-15 | | Release date: | 2021-11-03 | | Last modified: | 2024-01-31 | | Method: | X-RAY DIFFRACTION (2.01 Å) | | Cite: | Complementarity of neutron, XFEL and synchrotron crystallography for defining the structures of metalloenzymes at room temperature.
Iucrj, 9, 2022
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7XMC
 | | Cryo-EM structure of Cytochrome bo3 from Escherichia coli, apo structure with DMSO | | Descriptor: | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, COPPER (II) ION, Cytochrome bo(3) ubiquinol oxidase subunit 1, ... | | Authors: | Nishida, Y, Shigematsu, H, Iwamoto, T, Takashima, S, Shintani, Y. | | Deposit date: | 2022-04-25 | | Release date: | 2022-12-21 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (3.09 Å) | | Cite: | Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
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7XMD
 | | Cryo-EM structure of Cytochrome bo3 from Escherichia coli, the structure complexed with an allosteric inhibitor N4 | | Descriptor: | 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, COPPER (II) ION, Cytochrome bo(3) ubiquinol oxidase subunit 1, ... | | Authors: | Nishida, Y, Shigematsu, H, Iwamoto, T, Takashima, S, Shintani, Y. | | Deposit date: | 2022-04-25 | | Release date: | 2022-12-21 | | Last modified: | 2024-07-03 | | Method: | ELECTRON MICROSCOPY (2.99 Å) | | Cite: | Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
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7XMA
 | | Crystal structure of Bovine heart cytochrome c oxidase, apo structure with DMSO | | 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: | Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Takashima, S, Shintani, Y. | | Deposit date: | 2022-04-25 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
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7XMB
 | | Crystal structure of Bovine heart cytochrome c oxidase, the structure complexed with an allosteric inhibitor T113 | | 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: | Nishida, Y, Shinzawa-Itoh, K, Mizuno, N, Kumasaka, T, Yoshikawa, S, Tsukihara, T, Shintani, Y, Takashima, S. | | Deposit date: | 2022-04-25 | | Release date: | 2022-12-21 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.2 Å) | | Cite: | Identifying antibiotics based on structural differences in the conserved allostery from mitochondrial heme-copper oxidases.
Nat Commun, 13, 2022
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7XZK
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7DVU
 | | Crystal structure of heme sensor protein PefR in complex with heme and cyanide | | Descriptor: | CYANIDE ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.1 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVT
 | | Crystal structure of heme sensor protein PefR in complex with heme and carbon monoxide | | Descriptor: | CARBON MONOXIDE, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.09 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVR
 | | Crystal structure of heme sensor protein PefR from Streptococcus agalactiae in complex with heme | | Descriptor: | COBALT (II) ION, HTH marR-type domain-containing protein, PROTOPORPHYRIN IX CONTAINING FE | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2024-05-29 | | Method: | X-RAY DIFFRACTION (1.7 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVV
 | | Heme sensor protein PefR from Streptococcus agalactiae bound to operator DNA (28-mer) | | Descriptor: | DNA (28-MER), HTH marR-type domain-containing protein | | Authors: | Nishinaga, M, Nagai, S, Nishitani, Y, Sugimoto, H, Shiro, Y, Sawai, H. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.49 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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7DVS
 | | Crystal structure of Apo (heme-free) PefR | | Descriptor: | MarR family transcriptional regulator | | Authors: | Muraki, N, Aono, S. | | Deposit date: | 2021-01-15 | | Release date: | 2021-09-29 | | Last modified: | 2023-11-29 | | Method: | X-RAY DIFFRACTION (2.6 Å) | | Cite: | Heme controls the structural rearrangement of its sensor protein mediating the hemolytic bacterial survival.
Commun Biol, 4, 2021
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5Y89
 | | Periplasmic heme-binding protein BhuT in complex with one heme (holo-1) | | Descriptor: | ACETATE ION, PROTOPORPHYRIN IX CONTAINING FE, Putative hemin transport system, ... | | Authors: | Naoe, Y, Nakamura, N, Rahman, M.M, Shiro, Y, Sugimoto, H. | | Deposit date: | 2017-08-20 | | Release date: | 2017-10-11 | | Last modified: | 2024-03-27 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems
Proteins, 85, 2017
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5Y8B
 | | Periplasmic heme-binding protein RhuT from Roseiflexus sp. RS-1 in apo form | | Descriptor: | MAGNESIUM ION, Periplasmic binding protein | | Authors: | Rahman, M.M, Naoe, Y, Nakamura, N, Doi, A, Shiro, Y, Sugimoto, H. | | Deposit date: | 2017-08-20 | | Release date: | 2017-10-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.4 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems
Proteins, 85, 2017
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5Y8A
 | | Periplasmic heme-binding protein BhuT in complex with two hemes (holo-2 form) | | Descriptor: | CALCIUM ION, PROTOPORPHYRIN IX CONTAINING FE, Putative hemin transport system, ... | | Authors: | Nakamura, N, Naoe, Y, Rahman, M.M, Shiro, Y, Sugimoto, H. | | Deposit date: | 2017-08-20 | | Release date: | 2017-10-11 | | Last modified: | 2023-11-22 | | Method: | X-RAY DIFFRACTION (2.001 Å) | | Cite: | Structural basis for binding and transfer of heme in bacterial heme-acquisition systems
Proteins, 85, 2017
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