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Yorodumi- PDB-1d3g: HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d3g | ||||||
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Title | HUMAN DIHYDROOROTATE DEHYDROGENASE COMPLEXED WITH BREQUINAR ANALOG | ||||||
Components | DIHYDROOROTATE DEHYDROGENASE | ||||||
Keywords | OXIDOREDUCTASE / PROTEIN-ANTIPROLIFERATIVE AGENT COMPLEX | ||||||
Function / homology | Function and homology information pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Liu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 2000 Title: Structures of human dihydroorotate dehydrogenase in complex with antiproliferative agents. Authors: Liu, S. / Neidhardt, E.A. / Grossman, T.H. / Ocain, T. / Clardy, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d3g.cif.gz | 165.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d3g.ent.gz | 129.4 KB | Display | PDB format |
PDBx/mmJSON format | 1d3g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d3/1d3g ftp://data.pdbj.org/pub/pdb/validation_reports/d3/1d3g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39856.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET19B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02127, EC: 1.3.3.1 |
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-Non-polymers , 7 types, 280 molecules
#2: Chemical | ChemComp-SO4 / |
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#3: Chemical | ChemComp-ACT / |
#4: Chemical | ChemComp-BRE / |
#5: Chemical | ChemComp-FMN / |
#6: Chemical | ChemComp-ORO / |
#7: Chemical | ChemComp-DDQ / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.64 Å3/Da / Density % sol: 66.19 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: AMMONIUM SULFATE, ACETATE, GLYCEROL, DDAO, C11DAO, BREQUINAR, OROTATE, VAPOR DIFFUSION, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: CHESS / Beamline: A1 / Wavelength: 0.936 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.936 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. all: 77790 / Num. obs: 75457 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.6→1.7 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.21 / % possible all: 83.5 |
Reflection | *PLUS % possible obs: 97.1 % / Num. measured all: 444987 |
Reflection shell | *PLUS % possible obs: 84.8 % |
-Processing
Software |
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Refinement | Resolution: 1.6→30 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED WEIGHTED FULL MATRIX LEAST SQUARES PROCEDURE
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: REFMAC / Version: 4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.166 |