[English] 日本語
Yorodumi- PDB-4zl1: Crystal structure of human dihydroorotate dehydrogenase (DHODH) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zl1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18X at 1.86 A resolution | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrialDihydroorotate dehydrogenase (quinone) | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / complex / OXIDOREDUCTASE / 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: 1.86 Å | ||||||
Authors | Huang, J. / Wu, D. / Ouyang, P. / Lu, W. / Pu, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of human dihydroorotate dehydrogenase (DHODH) with 18XYW at 1.86 A resolution Authors: Huang, J. / Wu, D. / Ouyang, P. / Lu, W. / Pu, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4zl1.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4zl1.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zl1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zl/4zl1 ftp://data.pdbj.org/pub/pdb/validation_reports/zl/4zl1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 4jtuS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42636.414 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH / Plasmid: pET19b Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21-Gold(DE3)pLysS AG References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
---|
-Non-polymers , 5 types, 229 molecules
#2: Chemical | ChemComp-ORO / | ||
---|---|---|---|
#3: Chemical | ChemComp-FMN / | ||
#4: Chemical | ChemComp-18X / | ||
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.47 Å3/Da / Density % sol: 64.53 % |
---|---|
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, 1mM inhibitor PH range: 4.8-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 5, 2015 |
Radiation | Monochromator: MonochromatorSAGITALLY FOCUSED 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: 1.86→29.04 Å / Num. obs: 47711 / % possible obs: 99.86 % / Redundancy: 10.7 % / Net I/σ(I): 1.3 |
Reflection shell | Resolution: 1.86→1.908 Å / % possible all: 98.99 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JTU Resolution: 1.86→29.04 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.651 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 23.267 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.86→29.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|