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Yorodumi- PDB-5h2z: Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5h2z | ||||||
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Title | Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with 7GF | ||||||
Components | Dihydroorotate dehydrogenase (quinone), mitochondrial | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 | Wu, D. / Huang, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Human Dihydroorotate Dehydrogenase (DHODH) with 7GF 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 | 5h2z.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5h2z.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 5h2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5h2z_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5h2z_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5h2z_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5h2z_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/5h2z ftp://data.pdbj.org/pub/pdb/validation_reports/h2/5h2z | HTTPS FTP |
-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 29-395 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DHODH Production host: Escherichia coli O103:H2 str. 12009 (bacteria) Strain (production host): O103:H2 str. 12009 References: UniProt: Q02127, dihydroorotate dehydrogenase (quinone) |
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-Non-polymers , 6 types, 141 molecules
#2: Chemical | ChemComp-FMN / | ||||||
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#3: Chemical | ChemComp-ORO / | ||||||
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-7GF / | #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: 3.44 Å3/Da / Density % sol: 64.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 0.1M acetate, 40mM C11DAO, 20.8mM N,N-dimethyldecylamine-N-oxide (DDAO), 2mM DHO, 1.6-1.8 M ammonium sulfate 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: Apr 5, 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→41.09 Å / Num. obs: 76164 / % possible obs: 99.86 % / Redundancy: 16.3 % / Net I/σ(I): 4 |
Reflection shell | Resolution: 1.58→1.78 Å / CC1/2: 0.997 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JTU Resolution: 1.58→36.4 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 0.95 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.059 / 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: 25.213 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→36.4 Å
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Refine LS restraints |
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