+Open data
-Basic information
Entry | Database: PDB / ID: 1h7w | |||||||||
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Title | Dihydropyrimidine dehydrogenase (DPD) from pig | |||||||||
Components | DIHYDROPYRIMIDINE DEHYDROGENASE | |||||||||
Keywords | ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 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 / OTHER / Resolution: 1.9 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. | |||||||||
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 | 1h7w.cif.gz | 897.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h7w.ent.gz | 720 KB | Display | PDB format |
PDBx/mmJSON format | 1h7w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h7w_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 1h7w_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 1h7w_validation.xml.gz | 193.7 KB | Display | |
Data in CIF | 1h7w_validation.cif.gz | 291.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/1h7w ftp://data.pdbj.org/pub/pdb/validation_reports/h7/1h7w | HTTPS FTP |
-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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-Components
#1: Protein | Mass: 111603.344 Da / Num. of mol.: 4 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+) #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-FAD / #5: Water | ChemComp-HOH / | Compound details | INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE LEADING TO THE FORMATION OF BETA-ALANINE. ...INVOLVED IN THE CATABOLISM | Sequence details | RESIDUE GLY 60 IS EXCHANGED FOR ASP, AS COMPARED TO THE SEQUENCE DEPOSITED IN SWISS-PROT | |
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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 | |||||||||||||||
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: ESRF / Beamline: BM14 / Wavelength: 0.9184, 1.7392, 1.7416 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 15, 1999 | ||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→30 Å / Num. obs: 326433 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 9.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 10.9 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.24 / % possible all: 91.2 | ||||||||||||
Reflection | *PLUS Num. measured all: 2358836 / Rmerge(I) obs: 0.066 | ||||||||||||
Reflection shell | *PLUS % possible obs: 91.2 % / Rmerge(I) obs: 0.24 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.9→19.97 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 4006295.34 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE C-TERMINAL RESIDUE WAS NOT SEEN IN THE DENSITY MAPS
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 48 Å2 / ksol: 0.411635 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→19.97 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.007 / 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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LS refinement shell | *PLUS Rfactor Rfree: 0.2 |