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- PDB-8e4f: Crystal structure of dihydrofolate reductase (DHFR) from the fila... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8e4f | ||||||
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Title | Crystal structure of dihydrofolate reductase (DHFR) from the filarial nematode W. bancrofti in complex with NADPH and folate | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / Reductase | ||||||
Function / homology | ![]() glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lange, K. / Frey, K.M. / Goodey, N.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of dihydrofolate reductase from the filarial nematode W. bancrofti in complex with NADPH and folate. Authors: Lange, K. / Frey, K.M. / Eck, T. / Janson, C.A. / Gubler, U. / Goodey, N.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.8 KB | Display | ![]() |
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PDB format | ![]() | 38.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fzjS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 22381.811 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: WUBG_00817 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-NAP / | ||||
#3: Chemical | ChemComp-FOL / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.42 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 100 mM trisodium citrate pH (5.4-6.4), 25% w/v PEG 4000, and 200 mM ammonium sulfate PH range: 5.4-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 29, 2019 Details: double crystal Si(111) monochromator with horizontal axis | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.47→29.61 Å / Num. obs: 14828 / % possible obs: 99.7 % / Redundancy: 38.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.164 / Rpim(I) all: 0.027 / Rrim(I) all: 0.167 / Net I/σ(I): 24.8 / Num. measured all: 571238 / Scaling rejects: 2 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2FZJ Resolution: 2.47→29.61 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.3 Å2 / Biso mean: 34.4021 Å2 / Biso min: 15.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.47→29.61 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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