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Yorodumi- PDB-7lju: Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lju | ||||||
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Title | Porcine Dihydropyrimidine Dehydrogenase (DPD) crosslinked with 5-Ethynyluracil (5EU) | ||||||
Components | Dihydropyrimidine dehydrogenase [NADP(+)] | ||||||
Keywords | FLAVOPROTEIN / Dihydropyrimidine dehydrogenase / DPD / dehydrogenase / 5-Ethynyluracil / 5EU / inhibitor / inactivator / crosslinking | ||||||
Function / homology | Function and homology information dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding ...dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / flavin adenine dinucleotide binding / NADP binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å | ||||||
Authors | Butrin, A. / Forouzesh, D. / Beaupre, B. / Wawrzak, Z. / Liu, D. / Moran, G. | ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Authors: Forouzesh, D.C. / Beaupre, B.A. / Butrin, A. / Wawrzak, Z. / Liu, D. / Moran, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lju.cif.gz | 870 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lju.ent.gz | 699 KB | Display | PDB format |
PDBx/mmJSON format | 7lju.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lj/7lju ftp://data.pdbj.org/pub/pdb/validation_reports/lj/7lju | HTTPS FTP |
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-Related structure data
Related structure data | 7ljsC 7ljtC 1h7xS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ACDB
#1: Protein | Mass: 111603.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sus scrofa (pig) / Gene: DPYD / Production host: Escherichia coli (E. coli) References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+) |
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-Non-polymers , 6 types, 3421 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-Y3G / #5: Chemical | ChemComp-NAP / #6: Chemical | ChemComp-FNR / #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: DPD was crystallized by the vapor diffusion, hanging drop method by mixing 3 uL of 39 uM DPD in 25 mM HEPES, 2 mM DTT, 10% glycerol, pH 7.5 with 3 uL of well solution containing 100 mM NaCl, ...Details: DPD was crystallized by the vapor diffusion, hanging drop method by mixing 3 uL of 39 uM DPD in 25 mM HEPES, 2 mM DTT, 10% glycerol, pH 7.5 with 3 uL of well solution containing 100 mM NaCl, 2 mM DTT, 18% PEG 6000, pH 4.7. Rectangular hexahedron crystals grew in ~16-20 hours to a size of approximately 50 x 200 x 20 um. The crystals were soaked for 2 hours in 25 mM HEPES, 100 mM NaCl, 2 mM DTT, 100 uM NADPH, 100 uM 5EU, 20% PEG 6000, 20% PEG 400, pH 7.5. The whole procedure has been done anaerobically in the glove box. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1272 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Dec 9, 2020 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1272 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.87→45.46 Å / Num. obs: 336013 / % possible obs: 98.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.49 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.215 / Rpim(I) all: 0.117 / Net I/σ(I): 6.3 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1H7X Resolution: 1.87→40.59 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.37 / 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: 111.96 Å2 / Biso mean: 26.9761 Å2 / Biso min: 11.92 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.87→40.59 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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