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Yorodumi- PDB-4ls2: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ls2 | ||||||
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Title | Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A313 | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / oxidoreductase / FMN binding / mitochondria inner membrane / 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: 2.27 Å | ||||||
Authors | Zhu, L. / Li, H. / Ren, X. / Zhu, J. | ||||||
Citation | Journal: To be Published Title: Crystal structure of human dihydroorotate dehydrogenase (DHODH) with DH03A313 Authors: Zhu, L. / Li, H. / Ren, X. / Zhu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ls2.cif.gz | 92.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ls2.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ls2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ls2_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4ls2_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ls2_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 4ls2_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/4ls2 ftp://data.pdbj.org/pub/pdb/validation_reports/ls/4ls2 | HTTPS FTP |
-Related structure data
Related structure data | 1d3gS 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 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Production host: Escherichia coli (E. coli) References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 187 molecules
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | ChemComp-ORO / | ||||||
#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-3XS / | #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: 3.4 Å3/Da / Density % sol: 63.82 % |
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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 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 4, 2013 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→36.297 Å / Num. all: 34346 / Num. obs: 27386 / % possible obs: 79.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.17 Å2 |
Reflection shell | Resolution: 2.27→2.39 Å / % possible all: 99.95 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D3G Resolution: 2.27→33.012 Å / Occupancy max: 1 / Occupancy min: 0.19 / FOM work R set: 0.9047 / SU ML: 0.17 / σ(F): 1.6 / Phase error: 16.13 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 105.89 Å2 / Biso mean: 22.5429 Å2 / Biso min: 5.03 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.27→33.012 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: 10 / % reflection obs: 100 %
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