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- PDB-1gte: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WI... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1gte | |||||||||
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Title | DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WITH 5-IODOURACIL | |||||||||
![]() | DIHYDROPYRIMIDINE DEHYDROGENASE | |||||||||
![]() | OXIDOREDUCTASE / ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION | |||||||||
Function / homology | ![]() dihydropyrimidine dehydrogenase (NADP+) / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / uracil binding / beta-alanine biosynthetic process / thymine catabolic process / uracil catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide 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 / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y. | |||||||||
![]() | ![]() Title: Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. Authors: Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Crystallization and Preliminary X-Ray Study of Pig Liver Dihydropyrimidine Dehydrogenase Authors: Dobritzsch, D. / Persson, K. / Schneider, G. / Lindqvist, Y. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL, THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 895.2 KB | Display | ![]() |
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PDB format | ![]() | 720.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 198.7 KB | Display | |
Data in CIF | ![]() | 297.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 111603.344 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 4876 molecules ![](data/chem/img/SF4.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/IUR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMN.gif)
![](data/chem/img/FAD.gif)
![](data/chem/img/IUR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-IUR / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE LEADING TO THE FORMATION OF BETA-ALANINE. ...INVOLVED IN THE CATABOLISM |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 38.4 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 4.7 Details: 100 MM SODIUM CITRATE PH 4.7, 16-20 % POLYETHYLENE GLYCOL 6000, 1 MM DTT, 1 MM 5-IODOURACIL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion / Details: Dobritzsch, D., (2001) Acta Crystallogr., 57, 153. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8424 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. obs: 489160 / % possible obs: 98.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.65→1.74 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 4.3 / % possible all: 94.3 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. obs: 481684 |
Reflection shell | *PLUS % possible obs: 94.3 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, NON-LIGANDED FORM Resolution: 1.65→24.98 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3440087 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE 5 C-TERMINAL RESIDUES AND A FEW LOOP-RESIDUES WERE NOT SEEN IN THE DENSITY DUE TO DISORDER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.8663 Å2 / ksol: 0.394487 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→24.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.73 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 8
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Xplor file |
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.225 |