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Yorodumi- PDB-1ogk: The crystal structure of Trypanosoma cruzi dUTPase in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ogk | ||||||
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Title | The crystal structure of Trypanosoma cruzi dUTPase in complex with dUDP | ||||||
Components | DEOXYURIDINE TRIPHOSPHATASEDUTP diphosphatase | ||||||
Keywords | HYDROLASE / DIMER | ||||||
Function / homology | Function and homology information 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 Similarity search - Domain/homology | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 | 1ogk.cif.gz | 196.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ogk.ent.gz | 164.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ogk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/og/1ogk ftp://data.pdbj.org/pub/pdb/validation_reports/og/1ogk | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 32104.342 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: Y / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15923, dUTP diphosphatase #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 45.7 % | ||||||||||||||||||||||||
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Crystal grow | pH: 6.6 Details: 25% PEG 2000 MME, 0.3M SODIUM FORMATE, 50 MM SODIUM HEPES PH 7.0 | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 17 ℃ / pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||
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: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2001 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→20 Å / Num. obs: 27211 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.46 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.1 / % possible all: 97.3 |
Reflection | *PLUS Highest resolution: 2.85 Å / Lowest resolution: 20 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS Lowest resolution: 2.9 Å / % possible obs: 97.3 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 1.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NATIVE STRUCTURE Resolution: 2.85→111.8 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.881 / SU B: 19.26 / SU ML: 0.345 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ELEVATED B VALUES OF CHAIN D ATOMS REFLECT THE RELATIVE LACK OF STABILLISING CRYSTALLOGRAPHIC CONTACTS
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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: 34.97 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→111.8 Å
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Refine LS restraints |
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