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Open data
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Basic information
Entry | Database: PDB / ID: 1vi2 | ||||||
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Title | Crystal structure of shikimate-5-dehydrogenase with NAD | ||||||
![]() | Shikimate 5-dehydrogenase 2 | ||||||
![]() | OXIDOREDUCTASE / structural genomics | ||||||
Function / homology | ![]() quinate/shikimate dehydrogenase [NAD(P)+] / quinate 3-dehydrogenase (NADP+) activity / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / protein homodimerization activity 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.3 KB | Display | ![]() |
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PDB format | ![]() | 100.6 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 ![]() 1o6dC ![]() 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 ![]() 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: 33132.973 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P0A6D5, shikimate dehydrogenase (NADP+) #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.76 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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: 2.1→38.18 Å / Num. all: 32986 / Num. obs: 32986 / % possible obs: 98.7 % / Redundancy: 3.79 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.4 | ||||||||||||
Reflection shell | Resolution: 2.1→2.18 Å / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 3.6 / % possible all: 91.4 | ||||||||||||
Reflection | *PLUS Redundancy: 3.8 % | ||||||||||||
Reflection shell | *PLUS % possible obs: 91.4 % |
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Processing
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Refinement | Method to determine structure: Se-Met MAD phasing / Resolution: 2.1→38.18 Å / σ(F): 0
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Solvent computation | Solvent model: Babinet bulk solvent correction / Bsol: 344.954 Å2 / ksol: 0.903 e/Å3 | ||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.282 Å2
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Refine Biso | Class: all / Treatment: isotropic | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→38.18 Å
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Refine LS restraints |
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Software | *PLUS Version: 4 / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.3 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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