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- PDB-5z6k: High-pressure Crystal Structure Analysis of M20 loop closed DHFR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5z6k | |||||||||
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Title | High-pressure Crystal Structure Analysis of M20 loop closed DHFR at 400 MPa | |||||||||
![]() | Dihydrofolate reductase | |||||||||
![]() | OXIDOREDUCTASE / M20 loop closed form | |||||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Watanabe, N. / Nagae, T. / Yamada, H. | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 48.2 KB | Display | ![]() |
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PDB format | ![]() | 36.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 11 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4x5fC ![]() 4x5gC ![]() 4x5hC ![]() 4x5iC ![]() 4x5jC ![]() 5z6fC ![]() 5z6jC ![]() 5z6lC ![]() 5z6mC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18377.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FOL / |
#3: Chemical | ChemComp-NAP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 400, CaCl, imidazole buffer |
-Data collection
Diffraction | Mean temperature: 297 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 9, 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→48.99 Å / Num. obs: 14269 / % possible obs: 99 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.508 |
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Processing
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Refinement | Resolution: 1.802→48.99 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.07
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.802→48.99 Å
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Refine LS restraints |
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LS refinement shell |
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