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Yorodumi- PDB-1mdz: Crystal structure of ArnB aminotransferase with cycloserine and p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mdz | ||||||
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Title | Crystal structure of ArnB aminotransferase with cycloserine and pyridoxal 5' phosphate | ||||||
Components | ArnB aminotransferase | ||||||
Keywords | TRANSFERASE / type 1 aminotransferase fold | ||||||
Function / homology | Function and homology information UDP-4-amino-4-deoxy-L-arabinose aminotransferase / UDP-4-amino-4-deoxy-L-arabinose aminotransferase / polysaccharide biosynthetic process / lipopolysaccharide biosynthetic process / transaminase activity / lipid A biosynthetic process / pyridoxal phosphate binding / response to antibiotic Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.07 Å | ||||||
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. ...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. | ||||||
Citation | Journal: Structure / Year: 2002 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: Journal: Proteins / Year: 2005 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mdz.cif.gz | 84.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mdz.ent.gz | 66.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1mdz_validation.pdf.gz | 840.1 KB | Display | wwPDB validaton report |
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Full document | 1mdz_full_validation.pdf.gz | 846 KB | Display | |
Data in XML | 1mdz_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 1mdz_validation.cif.gz | 27.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/1mdz ftp://data.pdbj.org/pub/pdb/validation_reports/md/1mdz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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.) Salmonella typhimurium (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZNF3 |
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#2: Chemical | ChemComp-DCS / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.07→38.55 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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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: 0.25 | ||||||||||||||||||||
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 |