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Yorodumi- PDB-4ylw: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ylw | ||||||
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Title | Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Inhibitor / Rheumatoid Arthritis / Complex / OXIDOREDUCTASE-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: 1.79 Å | ||||||
Authors | Wu, D. / Ouyang, P. / Lu, W. / Huang, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human dihydroorotate dehydrogenase (DHODH) with No.33 compound Authors: Wu, D. / Ouyang, P. / Lu, W. / Huang, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ylw.cif.gz | 93.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ylw.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ylw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ylw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4ylw_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ylw_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 4ylw_validation.cif.gz | 26.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yl/4ylw ftp://data.pdbj.org/pub/pdb/validation_reports/yl/4ylw | HTTPS FTP |
-Related structure data
Related structure data | 4jtsS 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: 42636.414 Da / Num. of mol.: 1 / Fragment: UNP residues 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Plasmid: pET19B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 5 types, 167 molecules
#2: Chemical | ChemComp-52Y / | ||
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#3: Chemical | ChemComp-FMN / | ||
#4: Chemical | ChemComp-ORO / | ||
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.43 Å3/Da / Density % sol: 64.11 % / Description: Yellow cube like |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M acetate, 40mM UDAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8M ammonium sulfate PH range: 4.8-6.0 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2014 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→28.64 Å / Num. obs: 53848 / % possible obs: 99.89 % / Redundancy: 10.1 % / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 1.79→1.82 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 5.7 / % possible all: 99.89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JTS Resolution: 1.79→28.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.403 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→28.64 Å
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Refine LS restraints |
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