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Open data
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Basic information
Entry | Database: PDB / ID: 1o6d | ||||||
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Title | Crystal structure of a hypothetical protein | ||||||
![]() | Hypothetical UPF0247 protein TM0844 | ||||||
![]() | Structural genomics / unknown function | ||||||
Function / homology | ![]() 23S rRNA (pseudouridine1915-N3)-methyltransferase / rRNA (pseudouridine-N3-)-methyltransferase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Structural GenomiX | ||||||
![]() | ![]() 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 | ![]() | 46.2 KB | Display | ![]() |
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PDB format | ![]() | 32.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1o60C ![]() 1o61C ![]() 1o62C ![]() 1o63C ![]() 1o64C ![]() 1o65C ![]() 1o66C ![]() 1o67C ![]() 1o68C ![]() 1o69C ![]() 1o6bC ![]() 1o6cC ![]() 1vgtC ![]() 1vguC ![]() 1vgvC ![]() 1vgwC ![]() 1vgxC ![]() 1vgyC ![]() 1vgzC ![]() 1vh0C ![]() 1vh1C ![]() 1vh2C ![]() 1vh3C ![]() 1vh4C ![]() 1vh5C ![]() 1vh6C ![]() 1vh7C ![]() 1vh8C ![]() 1vh9C ![]() 1vhaC ![]() 1vhcC ![]() 1vhdC ![]() 1vheC ![]() 1vhfC ![]() 1vhgC ![]() 1vhjC ![]() 1vhkC ![]() 1vhlC ![]() 1vhmC ![]() 1vhoC ![]() 1vhqC ![]() 1vhsC ![]() 1vhtC ![]() 1vhuC ![]() 1vhvC ![]() 1vhwC ![]() 1vhxC ![]() 1vhyC ![]() 1vhzC ![]() 1vi0C ![]() 1vi1C ![]() 1vi2C ![]() 1vi3C ![]() 1vi4C ![]() 1vi5C ![]() 1vi6C ![]() 1vi8C ![]() 1vi9C ![]() 1viaC ![]() 1vicC ![]() 1vimC ![]() 1viqC ![]() 1visC ![]() 1viuC ![]() 1vivC ![]() 1vixC ![]() 1viyC ![]() 1vizC C: citing same article ( |
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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
#1: Protein | Mass: 18981.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.33 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS 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: MAD / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.66→18.96 Å / Num. all: 18899 / Num. obs: 18899 / % possible obs: 99 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.7 | |||||||||
Reflection shell | Resolution: 1.66→1.75 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.3 / % possible all: 99 | |||||||||
Reflection | *PLUS Rmerge(I) obs: 0.05 | |||||||||
Reflection shell | *PLUS % possible obs: 99 % |
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Processing
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Refinement | Method to determine structure: Se-Met MAD phasing / Resolution: 1.66→18.96 Å / σ(F): 0
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Solvent computation | Solvent model: Babinet bulk solvent correction / Bsol: 317.075 Å2 / ksol: 0.999 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.967 Å2
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Refine Biso | Class: all / Treatment: isotropic | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.66→18.96 Å
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Refine LS restraints |
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Refine LS restraints | *PLUS
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