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Yorodumi- PDB-1tve: Homoserine Dehydrogenase in complex with 4-(4-hydroxy-3-isopropyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tve | ||||||
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Title | Homoserine Dehydrogenase in complex with 4-(4-hydroxy-3-isopropylphenylthio)-2-isopropylphenol | ||||||
Components | Homoserine dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / antifungal / small molecule screening / amino acid biosynthesis | ||||||
Function / homology | Function and homology information aspartate family amino acid biosynthetic process / homoserine biosynthetic process / aspartate kinase activity / homoserine dehydrogenase / homoserine dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / NADP binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Ejim, L. / Mirza, I.A. / Capone, C. / Nazi, I. / Jenkins, S. / Chee, G.L. / Berghuis, A.M. / Wright, G.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2004 Title: New phenolic inhibitors of yeast homoserine dehydrogenase Authors: Ejim, L. / Mirza, I.A. / Capone, C. / Nazi, I. / Jenkins, S. / Chee, G.L. / Berghuis, A.M. / Wright, G.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tve.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tve.ent.gz | 115.7 KB | Display | PDB format |
PDBx/mmJSON format | 1tve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tv/1tve ftp://data.pdbj.org/pub/pdb/validation_reports/tv/1tve | HTTPS FTP |
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-Related structure data
Related structure data | 1ebuS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38413.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: hom6 / Plasmid: PET22B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P31116, homoserine dehydrogenase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.3 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9.5 Details: Ches, PEG 600, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0722 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0722 Å / Relative weight: 1 |
Reflection | Resolution: 3→35.24 Å / Num. obs: 14617 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EBU Resolution: 3→35.24 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 169416.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 108.669 Å2 / ksol: 0.323665 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→35.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
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Xplor file |
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