+Open data
-Basic information
Entry | Database: PDB / ID: 5h73 | ||||||
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Title | Crystal structure of human DHODH with 18F | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / Dihydroorotate dehydrogenase / OXIDOREDUCTASE-INHIBITOR 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 / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Huang, J. / Wu, D. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human DHODH with 18F at 1.58 Angstroms resolution Authors: Huang, J. / Wu, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5h73.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h73.ent.gz | 66.2 KB | Display | PDB format |
PDBx/mmJSON format | 5h73.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/5h73 ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h73 | HTTPS FTP |
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-Related structure data
Related structure data | 4jtuS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42636.414 Da / Num. of mol.: 1 / Fragment: UNP residues 30-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 154 molecules
#2: Chemical | ChemComp-7L7 / | ||||
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#3: Chemical | ChemComp-FMN / | ||||
#4: Chemical | ChemComp-ORO / | ||||
#5: Chemical | #6: Chemical | ChemComp-ACT / #7: 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: 3.45 Å3/Da / Density % sol: 64.34 % / Description: The yellow cube. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 30% glycerol, 2.4M Ammonium sulfate, PH4.8, 0.1M Acetate, 40mM UDAO, 20.8mM DDAO PH range: 4.8-5.2 / Temp details: 20 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: May 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→41.12 Å / Num. obs: 76331 / % possible obs: 99.77 % / Redundancy: 13.2 % / Net I/σ(I): 1.41 |
Reflection shell | Resolution: 1.82→1.87 Å / Mean I/σ(I) obs: 7.07 / CC1/2: 0.977 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JTU Resolution: 1.58→41.12 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.094 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.425 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→41.12 Å
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Refine LS restraints |
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