+Open data
-Basic information
Entry | Database: PDB / ID: 3gyf | ||||||
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Title | Human DHFR with Z-isomer in Orthorhombic lattice | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / human dihydrofolate reductase packing / Z-isomer furopyrimidine / NADP / One-carbon metabolism | ||||||
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 / G1/S-Specific Transcription ...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 / G1/S-Specific Transcription / folic acid metabolic process / 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: 1.7 Å | ||||||
Authors | Cody, V. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: The Z isomer of 2,4-diaminofuro[2,3-d]pyrimidine antifolate promotes unusual crystal packing in a human dihydrofolate reductase ternary complex. Authors: Cody, V. / Pace, J. / Lin, L. / Gangjee, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gyf.cif.gz | 59.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gyf.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 3gyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gy/3gyf ftp://data.pdbj.org/pub/pdb/validation_reports/gy/3gyf | HTTPS FTP |
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-Related structure data
Related structure data | 1u72S 3d7x S: Starting model for refinement |
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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
#1: Protein | Mass: 21480.723 Da / Num. of mol.: 1 / Fragment: DHFR domain Source method: isolated from a genetically manipulated source Details: recombinant clone / Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Production host: Escherichia coli (E. coli) / Strain (production host): pDS5 / References: UniProt: P00374, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-51P / | ||
#3: Chemical | ChemComp-NDP / | ||
#4: Chemical | #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 Å3/Da / Density % sol: 38.55 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 100 mM K2HPO4, pH 6.9, 30% saturated AS, 3% v/v ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 4, 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: 1.4→45.64 Å / Num. obs: 18919 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 9.8 % / Biso Wilson estimate: 24.6 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.036 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.014 / Mean I/σ(I) obs: 1.2 / Num. unique all: 4606 / Rsym value: 0.45 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1u72 Resolution: 1.7→31.4 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.905 / SU B: 2.831 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / ESU R: 0.158 / ESU R Free: 0.156 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.787 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→31.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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