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Open data
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Basic information
Entry | Database: PDB / ID: 6gde | ||||||
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Title | DIHYDROOROTASE FROM AQUIFEX AEOLICUS STANDARD (P,T) | ||||||
![]() | Dihydroorotase | ||||||
![]() | HYDROLASE / Dihydroorotase / Aquifex aeolicus / 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. | ||||||
![]() | ![]() 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 | ![]() | 84.6 KB | Display | ![]() |
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PDB format | ![]() | 62.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 417.4 KB | Display | ![]() |
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Full document | ![]() | 426.9 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6gddC ![]() 6gdfC ![]() 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.) ![]() ![]() Strain: VF5 / Gene: pyrC, aq_806 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51 % / Description: SQUARE PLATES WITH RE-ENTRANT FACES |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: ETHANOL 12%, PEG 400 4%, ACETATE, PH 4.6. DROP: 6 ML/G PROT. + RESERVOIR. CRISTALLIZATION IN MITEGEN PLATES FOR IN-SITU RECORDINGS |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 14, 2018 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97996 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.66 Å / Num. obs: 14798 / % possible obs: 73.1 % / Redundancy: 6.4 % / CC1/2: 0.991 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.055 / Rrim(I) all: 0.145 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.45→2.55 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1705 / CC1/2: 0.571 / Rpim(I) all: 0.428 / % possible all: 75.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1XRF Resolution: 2.45→45.66 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 6.614 / SU ML: 0.136 / Cross valid method: NONE / ESU R: 0.44 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.998 Å2
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Refinement step | Cycle: 1 / Resolution: 2.45→45.66 Å
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Refine LS restraints |
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