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- PDB-1rnj: Crystal structure of inactive mutant dUTPase complexed with subst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1rnj | ||||||
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Title | Crystal structure of inactive mutant dUTPase complexed with substrate analogue imido-dUTP | ||||||
![]() | Deoxyuridine 5'-triphosphate nucleotidohydrolase | ||||||
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Function / homology | ![]() dUTP catabolic process / dUMP biosynthetic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G. | ||||||
![]() | ![]() Title: Structural Insights into the Catalytic Mechanism of Phosphate Ester Hydrolysis by dUTPase. Authors: Barabas, O. / Pongracz, V. / Kovari, J. / Wilmanns, M. / Vertessy, B.G. #1: ![]() Title: Atomic resolution structure of Escherichia coli dUTPase determined ab initio Authors: Gonzalez, A. / Larsson, G. / Persson, R. / Cedergren-Zeppezauer, E. | ||||||
History |
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Remark 600 | HETEROGEN THE TRIS MOLECULES (TRS), WHICH HAVE INHERENT THREEFOLD SYMMETRY, ARE LOCATED ON A ...HETEROGEN THE TRIS MOLECULES (TRS), WHICH HAVE INHERENT THREEFOLD SYMMETRY, ARE LOCATED ON A CRYSTALLOGRAPHIC THREEFOLD AXIS IN THE PRESENT STRUCTURE. IN AN ASYMMETRIC UNIT THERE IS ONLY ONE THIRD OF THE MOLECULES AND THE COMPLETE MOLECULES ARE BUILT BY THREEFOLD CRYSTALLOGRAPHIC SYMMETRY IN THE CRYSTAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.8 KB | Display | ![]() |
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PDB format | ![]() | 34.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1rn8C ![]() 1sehC ![]() 1sylC ![]() 1euwS ![]() 1ro1 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y, x-y, z and 1-x+y, 1-x, z. |
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Components
#1: Protein | Mass: 16301.631 Da / Num. of mol.: 1 / Mutation: D90N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-MG / | ||
#3: Chemical | ChemComp-DUP / | ||
#4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.3 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 3350, sodium acetate, Tris, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2003 |
Radiation | Monochromator: Si111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.7→22 Å / Num. obs: 18342 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.32 % / Rsym value: 0.059 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 20.81 % / Mean I/σ(I) obs: 2 / Num. unique all: 1268 / Rsym value: 0.38 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1EUW Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.624 / SU ML: 0.054 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.091 / 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: 19.221 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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