[English] 日本語
Yorodumi- PDB-2qn4: Structure and function study of rice bifunctional alpha-amylase/s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2qn4 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure and function study of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa | ||||||
Components | Alpha-amylase/subtilisin inhibitor | ||||||
Keywords | HYDROLASE INHIBITOR / RASI / amylase inhibitor / subtilisin inhibitor / Alpha-amylase inhibitor / Protease inhibitor / Serine protease inhibitor | ||||||
Function / homology | Function and homology information alpha-amylase inhibitor activity / serine-type endopeptidase inhibitor activity Similarity search - Function | ||||||
Biological species | Oryza sativa subsp. japonica (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Peng, W.Y. / Lin, Y.H. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Chen, C.J. | ||||||
Citation | Journal: To be Published Title: Structure and Function Study of Rice Bifunctional Alpha-Amylase/Subtilisin Inhibitor from Oryza Sativa Authors: Peng, W.Y. / Lin, Y.H. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Liu, M.Y. / Chang, T. / Chen, C.J. #1: Journal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006 Title: Purification, crystallization and preliminary X-ray crystallographic analysis of rice bifunctional alpha-amylase/subtilisin inhibitor from Oryza sativa Authors: Lin, Y.H. / Peng, W.Y. / Huang, Y.C. / Guan, H.H. / Hsieh, Y.C. / Liu, M.Y. / Chang, T. / Chen, C.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2qn4.cif.gz | 77.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2qn4.ent.gz | 57.8 KB | Display | PDB format |
PDBx/mmJSON format | 2qn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qn/2qn4 ftp://data.pdbj.org/pub/pdb/validation_reports/qn/2qn4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1avaS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 21443.461 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Oryza sativa subsp. japonica (Japanese rice) Strain: japonica cultivar-group / References: UniProt: P29421 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.17 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7 Details: 20% PEG3350, 0.2M Potassium dihydrogen phosphate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2006 Details: Vertically Collimating Premirror, LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 31823 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rsym value: 0.062 / Net I/σ(I): 22.5654 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 5.25 / Num. unique all: 3129 / Rsym value: 0.363 / % possible all: 99.9 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AVA Resolution: 1.8→30 Å / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 0.16 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.86 Å
|