+Open data
-Basic information
Entry | Database: PDB / ID: 1ogl | ||||||
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Title | The crystal structure of native Trypanosoma cruzi dUTPase | ||||||
Components | DEOXYURIDINE TRIPHOSPHATASE | ||||||
Keywords | HYDROLASE / DUTPASE / TRYPANOSOMA CRUZI / NATIVE / DIMER | ||||||
Function / homology | all-alpha NTP pyrophosphatase / Type II deoxyuridine triphosphatase / all-alpha NTP pyrophosphatases / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Up-down Bundle / Mainly Alpha / Deoxyuridine triphosphatase Function and homology information | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Harkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The Crystal Structure of Trypanosoma Cruzi Dutpase Reveals a Novel Dutp/Dudp Binding Fold Authors: Harkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ogl.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogl.ent.gz | 45.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ogl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ogl_validation.pdf.gz | 426.5 KB | Display | wwPDB validaton report |
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Full document | 1ogl_full_validation.pdf.gz | 431.1 KB | Display | |
Data in XML | 1ogl_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1ogl_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogl ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogl | HTTPS FTP |
-Related 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: 32104.342 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: Y / Plasmid: PET-11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15923, dUTP diphosphatase |
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#2: 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: 2.9 Å3/Da / Density % sol: 57 % Description: ADDITIONAL PHASE INFORMATION PROVIDED THROUGH MERCURYL DERIVATIVE | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: 15% PEG 2000 MME, 0.1 M LISO4, 50 MM SODIUM CACODYLATE PH 6.6 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 290 K / pH: 6.6 / Method: vapor diffusion, hanging drop / Details: Harkiolaki, M., (2001) Acta Cryst., D57, 915. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9688 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 15, 2000 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9688 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→12 Å / Num. obs: 14827 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.4 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.1 / % possible all: 88.4 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.051 |
Reflection shell | *PLUS % possible obs: 88.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: LOW RESOLUTION MAD STRUCTURE Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.775 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.246 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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