[English] 日本語
Yorodumi- PDB-5z6j: High-pressure Crystal Structure Analysis of M20 loop closed DHFR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5z6j | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | High-pressure Crystal Structure Analysis of M20 loop closed DHFR at 220 MPa | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | OXIDOREDUCTASE / M20 loop closed form | |||||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.803 Å | |||||||||
Authors | Watanabe, N. / Nagae, T. / Yamada, H. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP. Authors: Nagae, T. / Yamada, H. / Watanabe, N. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5z6j.cif.gz | 48.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5z6j.ent.gz | 36.1 KB | Display | PDB format |
PDBx/mmJSON format | 5z6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/5z6j ftp://data.pdbj.org/pub/pdb/validation_reports/z6/5z6j | HTTPS FTP |
---|
-Related structure data
Related structure data | 4x5fC 4x5gC 4x5hC 4x5iC 4x5jC 5z6fC 5z6kC 5z6lC 5z6mC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18377.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase |
---|---|
#2: Chemical | ChemComp-FOL / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.57 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 400, CaCl, imidazole buffer |
-Data collection
Diffraction | Mean temperature: 297 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: AichiSR / Beamline: BL2S1 / Wavelength: 0.75 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 10, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.75 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→49.22 Å / Num. obs: 14502 / % possible obs: 99.4 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.398 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.803→49.219 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.03
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.803→49.219 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|