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Yorodumi- PDB-3uha: Crystal Structure of Saccharopine Dehydrogenase from Saccharomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3uha | ||||||
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Title | Crystal Structure of Saccharopine Dehydrogenase from Saccharomyces cervisiae complexed with NAD. | ||||||
Components | Saccharopine dehydrogenase [NAD+, L-lysine-forming] | ||||||
Keywords | OXIDOREDUCTASE / Lysine Biosynthesis / proton shuttle / enzyme mechanism / NAD binding | ||||||
Function / homology | Function and homology information saccharopine dehydrogenase (NAD+, L-lysine-forming) / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine biosynthetic process / protein import into peroxisome matrix / lysine biosynthetic process via aminoadipic acid / peroxisome / mRNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Cook, P.F. / Kumar, V.P. / Thomas, L.M. / West, A.H. / Bobyk, K.D. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Evidence in Support of Lysine 77 and Histidine 96 as Acid-Base Catalytic Residues in Saccharopine Dehydrogenase from Saccharomyces cerevisiae. Authors: Kumar, V.P. / Thomas, L.M. / Bobyk, K.D. / Andi, B. / Cook, P.F. / West, A.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3uha.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3uha.ent.gz | 121.2 KB | Display | PDB format |
PDBx/mmJSON format | 3uha.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uh/3uha ftp://data.pdbj.org/pub/pdb/validation_reports/uh/3uha | HTTPS FTP |
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-Related structure data
Related structure data | 3ugkSC 3uh1C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 41507.691 Da / Num. of mol.: 2 / Mutation: C205S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: LYS1, YIR034C / Plasmid: pET-16b / Production host: Escherichia coli (E. coli) References: UniProt: P38998, saccharopine dehydrogenase (NAD+, L-lysine-forming) #2: Chemical | #3: Chemical | ChemComp-CL / | #4: 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: 2.49 Å3/Da / Density % sol: 50.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M Bis-Tris Propane, 0.22M Malonate, 24% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 1, 2011 |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→32.64 Å / Num. all: 78060 / Num. obs: 35383 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1.5 / Redundancy: 2.2 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 5.3 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.632 / Mean I/σ(I) obs: 1.5 / Num. unique all: 5072 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 3UGK Resolution: 2.3→32.64 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.877 / SU B: 7.8 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.513 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→32.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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