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Yorodumi- PDB-1h7x: Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h7x | |||||||||
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Title | Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil | |||||||||
Components | DIHYDROPYRIMIDINE DEHYDROGENASE | |||||||||
Keywords | ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION / OXIDOREDUCTASE | |||||||||
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: 2.01 Å | |||||||||
Authors | Dobritzsch, D. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y. | |||||||||
Citation | Journal: Embo J. / Year: 2001 Title: Crystal Structure of Dihydropyrimidine Dehydrogenase, a Major Determinant of the Pharmacokinetics of the Anti-Cancer Drug 5-Fluorouracil Authors: Dobritzsch, D. / 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, DF" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF, BF, CF, DF" IN EACH CHAIN ON SHEET RECORDS ARE 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 | 1h7x.cif.gz | 894.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h7x.ent.gz | 719 KB | Display | PDB format |
PDBx/mmJSON format | 1h7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h7x ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h7x | 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: 111571.281 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) SUS SCROFA (pig) / Cellular location: CYTOPLASM / Gene: DPYD / Plasmid: PSE420 / Gene (production host): DPYD / Production host: Escherichia coli DH5[alpha] (bacteria) References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+) |
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-Non-polymers , 6 types, 4321 molecules
#2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-NDP / #6: Chemical | ChemComp-URF / #7: Water | ChemComp-HOH / | |
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-Details
Compound details | CHAIN A, B, C, D ENGINEERED MUTATION CYS671ALA INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE ...CHAIN A, B, C, D ENGINEERED |
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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: 2.4 Å3/Da / Density % sol: 50 % | |||||||||||||||
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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 NADPH, 5 MM 5FU | |||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||
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: MAX II / Beamline: I711 / Wavelength: 0.9746 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9746 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 274925 / % possible obs: 99 % / Redundancy: 2.8 % / Biso Wilson estimate: 8.7 Å2 / Rsym value: 0.063 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.166 / % possible all: 95.8 |
Reflection | *PLUS Num. measured all: 1471519 / Rmerge(I) obs: 0.063 |
Reflection shell | *PLUS % possible obs: 95.8 % / Rmerge(I) obs: 0.166 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, UNCOMPLEXED Resolution: 2.01→25.08 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 4072791.96 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE C-TERMINAL RESIDUES WERE NOT SEEN IN THE DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.371281 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.01→25.08 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 2 Å2 / Rms dev position: 0.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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