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- PDB-6gdf: DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 600 BAR OF HYDROSTATIC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6gdf | ||||||
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Title | DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 600 BAR OF HYDROSTATIC PRESSURE | ||||||
![]() | Dihydroorotase | ||||||
![]() | HYDROLASE / Dihydroorotase / Aquifex aeolicus / at 600 bar hydrostatic pressure / room temperature | ||||||
Function / homology | ![]() allantoinase activity / dihydroorotase / purine nucleobase catabolic process / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prange, T. / Girard, E. / Herve, G. / Evans, D.R. | ||||||
![]() | ![]() Title: Pressure-induced activation of latent dihydroorotase from Aquifex aeolicus as revealed by high pressure protein crystallography. Authors: Prange, T. / Girard, E. / Fourme, R. / Dhaussy, A.C. / Edwards, B. / Vaishnav, A. / Patel, C. / Guy-Evans, H. / Herve, G. / Evans, D.R. #1: Journal: J. Biol. Chem. / Year: 2017 Title: Activation of latent dihydroorotase from aquifex aeolicus by pressure Authors: Herve, G. / Guy-Evans, H. / Fernado, R. / Patel, C. / Hachem, F. / Evans, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.6 KB | Display | ![]() |
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PDB format | ![]() | 65.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431 KB | Display | ![]() |
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Full document | ![]() | 443.9 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gddC ![]() 6gdeC ![]() 1xrfS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46626.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62 % / Description: Prism, 0.2 mm |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ETHANOL (12%), PEG 400 (4%), ACETATE, PH 4.6 (0.1 M) |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 22, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3738 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.42 Å / Num. obs: 14277 / % possible obs: 76.8 % / Redundancy: 4.7 % / Biso Wilson estimate: 46.1 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.833 / Mean I/σ(I) obs: 1.7 / % possible all: 78.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XRF Resolution: 2.5→45.42 Å / Cor.coef. Fo:Fc: 0.958 / SU B: 6.304 / SU ML: 0.128 / Cross valid method: NONE / ESU R: 0.717 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 45.46 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.42 Å
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Refine LS restraints |
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