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Yorodumi- PDB-1ebu: HOMOSERINE DEHYDROGENASE COMPLEX WITH NAD ANALOGUE AND L-HOMOSERINE -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ebu | |||||||||
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Title | HOMOSERINE DEHYDROGENASE COMPLEX WITH NAD ANALOGUE AND L-HOMOSERINE | |||||||||
Components | HOMOSERINE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / homoserine / dehydrogenase / dinucleotide / ternary / analogue | |||||||||
Function / homology | Function and homology information aspartate family amino acid biosynthetic process / homoserine dehydrogenase / homoserine dehydrogenase activity / homoserine biosynthetic process / threonine biosynthetic process / methionine biosynthetic process / NAD+ binding / NADP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.6 Å | |||||||||
Authors | DeLaBarre, B. / Thompson, P.R. / Wright, G.D. / Berghuis, A.M. | |||||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2000 Title: Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases. Authors: DeLaBarre, B. / Thompson, P.R. / Wright, G.D. / Berghuis, A.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary X-ray diffraction studies of homoserine dehydrogenase from Saccharomyces cerevisiae Authors: DeLaBarre, B. / Jacques, S.L. / Pratt, C.E. / Wright, G.D. / Berghuis, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ebu.cif.gz | 282.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ebu.ent.gz | 229.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ebu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ebu_validation.pdf.gz | 788.5 KB | Display | wwPDB validaton report |
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Full document | 1ebu_full_validation.pdf.gz | 834.3 KB | Display | |
Data in XML | 1ebu_validation.xml.gz | 59 KB | Display | |
Data in CIF | 1ebu_validation.cif.gz | 80.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/1ebu ftp://data.pdbj.org/pub/pdb/validation_reports/eb/1ebu | 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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Details | The asymmetric unit contains 2 dimers: A/B and C/D. The ternary complex is found in the D chain protomer |
-Components
#1: Protein | Mass: 38413.766 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: HOM6P / Production host: Escherichia coli (E. coli) / References: UniProt: P31116, homoserine dehydrogenase #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-NDA / | #4: Chemical | ChemComp-HSE / | #5: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.74 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8K, L-homoserine, 3-aminopyridine dinucleotide, sodium cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 218 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Feb 22, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. all: 44409 / Num. obs: 164716 / % possible obs: 99.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 35.4 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.344 / Num. unique all: 4392 / % possible all: 98.1 |
Reflection | *PLUS |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Resolution: 2.6→39.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1625863.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Model refined against amplitudes
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34 Å2 / ksol: 0.322 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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