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- PDB-2axq: Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2axq | ||||||
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Title | Apo histidine-tagged saccharopine dehydrogenase (L-Glu forming) from Saccharomyces cerevisiae | ||||||
![]() | Saccharopine dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / ROSSMANN FOLD VARIANT / SACCHAROPINE REDUCTASE FOLD (DOMAIN II) / ALPHA/BETA PROTEIN / ALPHA-AMINOADIPATE PATHWAY / FUNGAL LYSINE BIOSYNTHESIS | ||||||
Function / homology | ![]() saccharopine dehydrogenase (NADP+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / lysine biosynthetic process via aminoadipic acid / cell periphery / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Andi, B. / Cook, P.F. / West, A.H. | ||||||
![]() | ![]() Title: Crystal structure of the his-tagged saccharopine reductase from Saccharomyces cerevisiae at 1.7-A resolution. Authors: Andi, B. / Cook, P.F. / West, A.H. #1: ![]() Title: Crystal Structure of Saccharopine Reductase from Magnaporthe Grisea, an Enzyme of the Alpha-Aminoadipate Pathway of Lysine Biosynthesis Authors: Johansson, E. / Steffens, J.J. / Lindqvist, Y. / Schneider, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.7 KB | Display | ![]() |
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PDB format | ![]() | 81.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 440.4 KB | Display | ![]() |
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Full document | ![]() | 441.3 KB | Display | |
Data in XML | ![]() | 20.8 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e5lS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a homodimer generated from the monomer in the asymmetric unit by the operations: y, x, -z |
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Components
#1: Protein | Mass: 51505.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: L-Glu forming Source: (gene. exp.) ![]() ![]() Gene: LYS9, LYS13 / Plasmid: pET-16b-LYS9 / Production host: ![]() ![]() References: UniProt: P38999, saccharopine dehydrogenase (NADP+, L-glutamate-forming) | ||
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#2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 1.2M Ammonium sulfate, 25mM Bis-Tris, 6.5-7mg/mL enzyme, 50mM Tris-HCl pH 8.0, 150mM KCl, 75mM imidazole, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 18, 2003 / Details: MICRO-OPTICS |
Radiation | Monochromator: OSMIC CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→39.85 Å / Num. all: 66370 / Num. obs: 64775 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 7.18 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.056 / Χ2: 1 / Net I/σ(I): 15.8 / Scaling rejects: 3516 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible obs: 95.9 % / Redundancy: 4.98 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.3 / Num. measured obs: 324 / Num. unique all: 6559 / Χ2: 1.16 / % possible all: 95.9 |
-Phasing
Phasing MR |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E5L, used monomer, backbone only Resolution: 1.7→39.85 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.661 / SU ML: 0.084 / Isotropic thermal model: Mixed (isotropic/anisotropic) / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.099 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The first methionine residue and N-terminal deca-histidine tag could not be built because of missing electron density.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.461 Å2
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Refine analyze | Luzzati coordinate error obs: 0.219 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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