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Yorodumi- PDB-5k9d: Crystal structure of human dihydroorotate dehydrogenase at 1.7 A ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5k9d | ||||||
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Title | Crystal structure of human dihydroorotate dehydrogenase at 1.7 A resolution | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE / alpha/beta barrel | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | ||||||
Authors | Lewis, T.A. / Sykes, D.B. / Law, J.M. / Munoz, B. / Scadden, D.T. / Rustiguel, J.K. / Nonato, M.C. / Schreiber, S.L. | ||||||
Citation | Journal: ACS Med Chem Lett / Year: 2016 Title: Development of ML390: A Human DHODH Inhibitor That Induces Differentiation in Acute Myeloid Leukemia. Authors: Lewis, T.A. / Sykes, D.B. / Law, J.M. / Munoz, B. / Rustiguel, J.K. / Nonato, M.C. / Scadden, D.T. / Schreiber, S.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5k9d.cif.gz | 228.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5k9d.ent.gz | 182.5 KB | Display | PDB format |
PDBx/mmJSON format | 5k9d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5k9d_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5k9d_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5k9d_validation.xml.gz | 21 KB | Display | |
Data in CIF | 5k9d_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/5k9d ftp://data.pdbj.org/pub/pdb/validation_reports/k9/5k9d | HTTPS FTP |
-Related structure data
Related structure data | 5k9cC 1d3gS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39943.613 Da / Num. of mol.: 1 / Fragment: residues 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Plasmid: pET28a / Details (production host): pET28a modified vector / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 8 types, 407 molecules
#2: Chemical | ChemComp-FNR / | ||||||||
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#3: Chemical | ChemComp-ORO / | ||||||||
#4: Chemical | ChemComp-CE9 / | ||||||||
#5: Chemical | #6: Chemical | #7: Chemical | #8: Chemical | ChemComp-GOL / | #9: 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: 3.46 Å3/Da / Density % sol: 64.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.8 Details: 0.1 M sodium acetate trihydrate pH 4.8 1.8 M ammonium sulfate 30% (v/v) glycerol PH range: 4.8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45867 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 10, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double-crystal monochromator and toroidal bendable mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.45867 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→28.18 Å / Num. obs: 63435 / % possible obs: 99.7 % / Redundancy: 14.3 % / Biso Wilson estimate: 12.56 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/av σ(I): 4.864 / Net I/σ(I): 16.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D3G Resolution: 1.7→26.568 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 117.19 Å2 / Biso mean: 19.4203 Å2 / Biso min: 3.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→26.568 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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