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- PDB-1vhn: Crystal structure of a putative flavin oxidoreductase with flavin -
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Open data
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Basic information
Entry | Database: PDB / ID: 1vhn | ||||||
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Title | Crystal structure of a putative flavin oxidoreductase with flavin | ||||||
![]() | putative flavin oxidoreductase | ||||||
![]() | Structural genomics / unknown function | ||||||
Function / homology | ![]() tRNA dihydrouridine synthase activity / Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor / flavin adenine dinucleotide binding / RNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Structural GenomiX | ||||||
![]() | ![]() Title: The 1.59 A resolution crystal structure of TM0096, a flavin mononucleotide binding protein from Thermotoga maritima. Authors: Park, F. / Gajiwala, K. / Noland, B. / Wu, L. / He, D. / Molinari, J. / Loomis, K. / Pagarigan, B. / Kearins, P. / Christopher, J. / Peat, T. / Badger, J. / Hendle, J. / Lin, J. / Buchanan, S. #1: ![]() Title: Structural analysis of a set of proteins resulting from a bacterial genomics project Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / ...Authors: Badger, J. / Sauder, J.M. / Adams, J.M. / Antonysamy, S. / Bain, K. / Bergseid, M.G. / Buchanan, S.G. / Buchanan, M.D. / Batiyenko, Y. / Christopher, J.A. / Emtage, S. / Eroshkina, A. / Feil, I. / Furlong, E.B. / Gajiwala, K.S. / Gao, X. / He, D. / Hendle, J. / Huber, A. / Hoda, K. / Kearins, P. / Kissinger, C. / Laubert, B. / Lewis, H.A. / Lin, J. / Loomis, K. / Lorimer, D. / Louie, G. / Maletic, M. / Marsh, C.D. / Miller, I. / Molinari, J. / Muller-Dieckmann, H.J. / Newman, J.M. / Noland, B.W. / Pagarigan, B. / Park, F. / Peat, T.S. / Post, K.W. / Radojicic, S. / Ramos, A. / Romero, R. / Rutter, M.E. / Sanderson, W.E. / Schwinn, K.D. / Tresser, J. / Winhoven, J. / Wright, T.A. / Wu, L. / Xu, J. / Harris, T.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 83.5 KB | Display | ![]() |
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PDB format | ![]() | 60.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 785.5 KB | Display | ![]() |
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Full document | ![]() | 789 KB | Display | |
Data in XML | ![]() | 16.8 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 36895.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-FMN / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 21 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→30.85 Å / Num. all: 48147 / Num. obs: 48147 / % possible obs: 99.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 3.7 / % possible all: 94.5 |
Reflection | *PLUS Redundancy: 7 % / Num. measured all: 338732 |
Reflection shell | *PLUS % possible obs: 94.5 % |
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Processing
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Refinement | Method to determine structure: Se-Met SAD phasing / Resolution: 1.59→30.85 Å / σ(F): 0
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Solvent computation | Solvent model: Babinet bulk solvent correction / Bsol: 334.041 Å2 / ksol: 0.999 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.751 Å2
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Refine Biso | Class: all / Treatment: isotropic | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→30.85 Å
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Refine LS restraints |
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Software | *PLUS Version: 4 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 48147 / Num. reflection Rfree: 2351 / Rfactor obs: 0.187 / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.178 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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