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Yorodumi- PDB-4m6k: Crystal structure of human dihydrofolate reductase (DHFR) bound t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4m6k | ||||||
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Title | Crystal structure of human dihydrofolate reductase (DHFR) bound to NADP+ and folate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Rossmann Fold / NADPH binding / folate binding | ||||||
Function / homology | Function and homology information regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / folic acid 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 / dihydrofolate metabolic process / axon regeneration / folic acid binding / folic acid metabolic process / G1/S-Specific Transcription / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.396 Å | ||||||
Authors | Bhabha, G. / Ekiert, D.C. / Wright, P.E. / Wilson, I.A. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Authors: Bhabha, G. / Ekiert, D.C. / Jennewein, M. / Zmasek, C.M. / Tuttle, L.M. / Kroon, G. / Dyson, H.J. / Godzik, A. / Wilson, I.A. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4m6k.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4m6k.ent.gz | 83.4 KB | Display | PDB format |
PDBx/mmJSON format | 4m6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/4m6k ftp://data.pdbj.org/pub/pdb/validation_reports/m6/4m6k | HTTPS FTP |
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-Related structure data
Related structure data | 4m6jSC 4m6lC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 21480.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Plasmid: pET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/PDNAY / References: UniProt: P00374, dihydrofolate reductase |
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#2: Chemical | ChemComp-FOL / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.87 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 2 M ammonium sulfate, 100 mM phosphate/citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2009 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.396→50 Å / Num. obs: 44528 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 19.3 % / Rsym value: 0.08 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 1.396→1.42 Å / Redundancy: 19.3 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.79 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4M6J Resolution: 1.396→23.77 Å / SU ML: 0.16 / σ(F): 1.33 / Phase error: 17.42 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.396→23.77 Å
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Refine LS restraints |
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LS refinement shell |
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