[English] 日本語
Yorodumi- PDB-3e5r: Crystal structure and Functional Analysis of Glyceraldehyde-3-pho... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e5r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa | ||||||
Components | Glyceraldehyde-3-phosphate dehydrogenase, cytosolic | ||||||
Keywords | OXIDOREDUCTASE / GAPDH / Glyceraldehyde-3-phosphate / Oryza Sativa / rice / Cytoplasm / Glycolysis / NAD | ||||||
Function / homology | Function and homology information glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å | ||||||
Authors | Tien, Y.C. / Lin, Y.H. / Chang, S.L. / Chen, C.J. | ||||||
Citation | Journal: To be published Title: Crystal structure and Functional Analysis of Glyceraldehyde-3-phosphate Dehydrogenase from Oryza Sativa Authors: Tien, Y.C. / Lin, Y.H. / Chang, S.L. / Chen, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3e5r.cif.gz | 250.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3e5r.ent.gz | 200.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e5r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e5r_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3e5r_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3e5r_validation.xml.gz | 60.6 KB | Display | |
Data in CIF | 3e5r_validation.cif.gz | 84.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/3e5r ftp://data.pdbj.org/pub/pdb/validation_reports/e5/3e5r | HTTPS FTP |
-Related structure data
Related structure data | 3e6aC 1u8fS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36458.609 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa subsp. japonica (Japanese rice) Strain: Japonica cultivar-group / Gene: GAPDH / Plasmid: pET-sumo / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q0J8A4, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.1 Details: 0.1M citric acid, 16%(w/v) PEG3350, pH4.1, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å |
Detector | Detector: CCD / Date: Apr 9, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 57264 / Num. obs: 57264 / Redundancy: 3.3 % / Rsym value: 0.162 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: PDB ENTRY 1U8F Resolution: 2.3→30 Å / Occupancy max: 1 / Occupancy min: 0.3
| |||||||||||||||||||||||||
Displacement parameters | Biso max: 0.5 Å2 / Biso mean: 0.055 Å2 / Biso min: 0.01 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.38 Å
|