[English] 日本語
Yorodumi- PDB-3e9q: Crystal Structure of the Short Chain Dehydrogenase from Shigella ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3e9q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri | ||||||
Components | Short-chain dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / alpha-beta-alpha sandwich / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shigella flexneri 2a (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the Short Chain Dehydrogenase from Shigella flexneri Authors: Kim, Y. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3e9q.cif.gz | 228.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3e9q.ent.gz | 191.8 KB | Display | PDB format |
PDBx/mmJSON format | 3e9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e9q_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3e9q_full_validation.pdf.gz | 481.5 KB | Display | |
Data in XML | 3e9q_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 3e9q_validation.cif.gz | 38.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/3e9q ftp://data.pdbj.org/pub/pdb/validation_reports/e9/3e9q | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 30997.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal 6 His tag with TEV protease cut site / Source: (gene. exp.) Shigella flexneri 2a (bacteria) / Strain: 301 / Gene: yciK, S1358, SF1273 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q83RM3, UniProt: A0A0H2UYY2*PLUS |
---|
-Non-polymers , 5 types, 431 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.95 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Na Hepes pH 7.5, 1.5 ammonium sulphate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→38.9 Å / Num. all: 53859 / Num. obs: 53859 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2716 / % possible all: 99.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.7→38.8 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
| |||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.19 Å | |||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→38.8 Å
| |||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.73 Å
|