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Yorodumi- PDB-1gt8: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gt8 | |||||||||
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Title | DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID | |||||||||
Components | DIHYDROPYRIMIDINE DEHYDROGENASE | |||||||||
Keywords | OXIDOREDUCTASE / ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION | |||||||||
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 / 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 | SUS SCROFA (pig) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y. | |||||||||
Citation | Journal: J. Biol. Chem. / Year: 2002 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gt8.cif.gz | 792.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gt8.ent.gz | 645.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/1gt8 ftp://data.pdbj.org/pub/pdb/validation_reports/gt/1gt8 | HTTPS FTP |
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-Related 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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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.) SUS SCROFA (pig) / Organ: LIVER / Plasmid: PSE420 / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+) |
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-Non-polymers , 5 types, 32 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-NDP / #6: Chemical | ChemComp-UAA / |
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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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 40.03 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: 100 MM SODIUM CITRATE PH 4.7, 16-20% POLYETHYLENE GLYCOL 6000, 1 MM DTT | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 4.7 / 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: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 12, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→30 Å / Num. obs: 62722 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.6 / % possible all: 92.9 |
Reflection | *PLUS Highest resolution: 3.3 Å / Rmerge(I) obs: 0.098 |
Reflection shell | *PLUS Highest resolution: 3.3 Å / % possible obs: 92.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, TERNARY COMPLEX WITH 5-IODOURACIL AND NADPH, PH 7.5 Resolution: 3.3→29.75 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2857472 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE 6-8 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: 10 Å2 / ksol: 0.230877 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→29.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 2 Å2 / Rms dev position: 0.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.45 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Rfactor obs: 0.217 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.217 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.294 |