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- PDB-3f8y: Correlations of Human Dihydrofolate Reductase with Structural Dat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f8y | ||||||
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Title | Correlations of Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / active site mutants ligand complex DHFR / NADP / One-carbon metabolism | ||||||
Function / homology | ![]() regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A. | ||||||
![]() | ![]() Title: Correlations of Inhibitor Kinetics for Pneumocystis jirovecii and Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes. Authors: Cody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.5 KB | Display | ![]() |
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PDB format | ![]() | 45.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1008.5 KB | Display | ![]() |
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Full document | ![]() | 1013 KB | Display | |
Data in XML | ![]() | 15.6 KB | Display | |
Data in CIF | ![]() | 23.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f8zC ![]() 3f91C ![]() 3fs6C ![]() 1u72S S: Starting model for refinement 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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Unit cell |
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Components
#1: Protein | Mass: 21481.773 Da / Num. of mol.: 1 / Mutation: Q35K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-DH1 / | ||
#3: Chemical | ChemComp-NDP / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.83 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM potassium phosphate, pH 6.9, 30% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 6, 2008 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→53.3 Å / Num. obs: 50420 / % possible obs: 79.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.046 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.45→1.53 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 0.9 / Num. unique all: 1654 / Rsym value: 0.562 / % possible all: 98.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1u72 Resolution: 1.45→26.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.12 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.698 Å2
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Refine analyze | Luzzati coordinate error obs: 0.159 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.45→26.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
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