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- PDB-1mdz: Crystal structure of ArnB aminotransferase with cycloserine and p... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1mdz | ||||||
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Title | Crystal structure of ArnB aminotransferase with cycloserine and pyridoxal 5' phosphate | ||||||
![]() | ArnB aminotransferase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Noland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T. / Rutter, M.E. / Sanderson, W.E. ...Noland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T. / Rutter, M.E. / Sanderson, W.E. / Muller-Dieckmann, H.-J. / Gajiwala, K.S. / Sauder, J.M. / Buchanan, S.G. | ||||||
![]() | ![]() Title: Structural studies of Salmonella typhimurium ArnB (PmrH) aminotransferase: A 4-amino-4-deoxy-L-arabinose lipopolysaccharide modifying enzyme Authors: Noland, B.W. / Newman, J.M. / Hendle, J. / Badger, J. / Christopher, J.A. / Tresser, J. / Buchanan, M.D. / Wright, T. / Rutter, M.E. / Sanderson, W.E. / Muller-Dieckmann, H.-J. / Gajiwala, K. / Buchanan, S.G. #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.R. | ||||||
History |
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Remark 600 | HETEROGEN THE USE OF ALTERNATE CONFORMATION ID IN DCS AND PLP IN THIS ENTRY IS NOT TO INDICATE THAT ...HETEROGEN THE USE OF ALTERNATE CONFORMATION ID IN DCS AND PLP IN THIS ENTRY IS NOT TO INDICATE THAT THE ATOMS SPECIFIED HAVE MORE THAN ONE IDENTIFIABLE SITE. THERE IS ONLY ONE SITE FOR EACH ATOM IN DCS AND PLP, ALTHOUGH THE SITES HAVE PARTIAL OCCUPANCIES BECAUSE THE TWO LIGANDS ARE COMPETING FOR THE SAME SPACE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.4 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42831.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-DCS / |
#3: Chemical | ChemComp-PLP / ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.04 % | ||||||||||||||||||||||||||||||
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 Details: sodium citrate, PEG 10000, beta-mercaptoethanol, pH 5.5, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.07→38.55 Å / Num. all: 33311 / Num. obs: 33311 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.07→2.18 Å / % possible all: 91.7 |
Reflection | *PLUS Highest resolution: 2.08 Å / Lowest resolution: 38.6 Å / % possible obs: 99.4 % / Redundancy: 13.2 % / Num. measured all: 440660 / Rmerge(I) obs: 0.2 |
Reflection shell | *PLUS % possible obs: 96.3 % / Redundancy: 8.6 % / Rmerge(I) obs: 1.419 / Mean I/σ(I) obs: 2.4 |
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Processing
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Refinement | Method to determine structure![]() ![]()
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Refinement step | Cycle: LAST / Resolution: 2.07→38.55 Å
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Refinement | *PLUS Highest resolution: 2.08 Å / Lowest resolution: 38.55 Å / Rfactor obs: 0.223 / Rfactor Rfree![]() | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.08 Å / Lowest resolution: 5 Å / Num. reflection obs: 30476 |