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Yorodumi- PDB-6gdd: DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 1200 BAR OF HYDROSTATI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gdd | ||||||
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Title | DIHYDROOROTASE FROM AQUIFEX AEOLICUS UNDER 1200 BAR OF HYDROSTATIC PRESSURE | ||||||
Components | Dihydroorotase | ||||||
Keywords | HYDROLASE / Dihydroorotase / Aquifex aeolicus / hydrostatic pressure / room temperature | ||||||
Function / homology | Function and homology information allantoinase activity / purine nucleobase catabolic process / dihydroorotase / dihydroorotase activity / 'de novo' UMP biosynthetic process / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å | ||||||
Authors | Prange, T. / Girard, E. / Herve, G. / Evans, D.R. | ||||||
Citation | Journal: Febs J. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gdd.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gdd.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 6gdd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gd/6gdd ftp://data.pdbj.org/pub/pdb/validation_reports/gd/6gdd | HTTPS FTP |
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-Related structure data
Related structure data | 6gdeC 6gdfC 1xrfS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 46440.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria) Strain: VF5 / Gene: pyrC, aq_806 / Production host: Escherichia coli (E. coli) / References: UniProt: O66990, dihydroorotase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 3.17 Å3/Da / Density % sol: 61.19 % / Description: prism |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: ETHANOL (12%), PEG 400 (4%), ACETATE BUFFER (0.1M). PROTEIN 6 MG/ML |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID27 / Wavelength: 0.3738 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 22, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.3738 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→45.33 Å / Num. obs: 20901 / % possible obs: 99.6 % / Redundancy: 7.1 % / Biso Wilson estimate: 49.2 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.062 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.17 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3014 / Rpim(I) all: 0.46 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1XRF Resolution: 2.6→40.3 Å / Cor.coef. Fo:Fc: 0.965 / SU B: 6.238 / SU ML: 0.125 / Cross valid method: NONE / ESU R: 0.337 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.645 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→40.3 Å
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Refine LS restraints |
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