[English] 日本語
Yorodumi- PDB-2qrj: Crystal Structure of Sulfate-bound Saccharopine Dehydrogenase (L-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qrj | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Sulfate-bound Saccharopine Dehydrogenase (L-Lys Forming) from Saccharomyces cerevisiae | ||||||
Components | Saccharopine dehydrogenase, NAD+, L-lysine-forming | ||||||
Keywords | OXIDOREDUCTASE / Sulfate / Rossmann fold / alpha-aminoadipate pathway / fungal lysine biosynthesis / Acetylation / Amino-acid biosynthesis / Cytoplasm / NAD | ||||||
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 / molecular replacement / Resolution: 1.6 Å | ||||||
Authors | Andi, B. / Xu, H. / Cook, P.F. / West, A.H. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Crystal Structures of Ligand-Bound Saccharopine Dehydrogenase from Saccharomyces cerevisiae Authors: Andi, B. / Xu, H. / Cook, P.F. / West, A.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qrj.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qrj.ent.gz | 69.6 KB | Display | PDB format |
PDBx/mmJSON format | 2qrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2qrj_validation.pdf.gz | 445.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2qrj_full_validation.pdf.gz | 449.8 KB | Display | |
Data in XML | 2qrj_validation.xml.gz | 18.7 KB | Display | |
Data in CIF | 2qrj_validation.cif.gz | 28 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/2qrj ftp://data.pdbj.org/pub/pdb/validation_reports/qr/2qrj | HTTPS FTP |
-Related structure data
Related structure data | 2qrkC 2qrlC 2q99S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 44057.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: LYS1 / Plasmid: pSDHHX1 (pET16b derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL References: UniProt: P38998, saccharopine dehydrogenase (NAD+, L-lysine-forming) | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.2 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: PEG-MME 2000, Tris, (NH4)2SO4, pH 7.0, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 8, 2005 / 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: 1.6→28.75 Å / Num. all: 54642 / Num. obs: 53059 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.71 % / Biso Wilson estimate: 33.9 Å2 / Rmerge(I) obs: 0.06 / Χ2: 1 / Net I/σ(I): 11.3 / Scaling rejects: 2693 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q99 (BACKBONE ONLY) Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.43 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 29.498 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.224 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
|