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- PDB-3tp1: Crystal Structure of the precatalytic M-PMV dUTPase - substrate (... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tp1 | ||||||
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Title | Crystal Structure of the precatalytic M-PMV dUTPase - substrate (dUPNPP) complex | ||||||
![]() | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE | ||||||
![]() | HYDROLASE / jelly roll | ||||||
Function / homology | ![]() dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral process / viral nucleocapsid / structural constituent of virion / aspartic-type endopeptidase activity / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Barabas, O. / Nemeth, V. / Vertessy, B.G. | ||||||
![]() | ![]() Title: Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize In-line Attack and Inversion Authors: Barabas, O. / Nemeth, V. / Bodor, A. / Perczel, A. / Rosta, E. / Kele, Z. / Zagyva, I. / Szabadka, Z. / Grolmusz, V.I. / Wilmanns, M. / Vertessy, B.G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2006 Title: Crystallization and preliminary X-ray studies of dUTPase from Mason-Pfizer monkey retrovirus. Authors: Barabas, O. / Nemeth, V. / Vertessy, B.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63.1 KB | Display | ![]() |
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PDB format | ![]() | 44.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3tpnC ![]() 3tpsC ![]() 3tpwC ![]() 3tpyC ![]() 3tq3C ![]() 3tq4C ![]() 3tq5C ![]() 3trlC ![]() 2d4lS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 16171.373 Da / Num. of mol.: 1 / Fragment: dUTPase (catalytic) domain, UNP residues 608-759 / Mutation: N83K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O92810, UniProt: P07570*PLUS, dUTP diphosphatase |
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#2: Chemical | ChemComp-DUP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 26, 2005 / Details: BENT, VERTICALLY FOCUSING MIRROR |
Radiation | Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8034 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→20 Å / Num. all: 17501 / Num. obs: 17501 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.04 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2371 / Rsym value: 0.32 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB entry 2D4L Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.756 / SU ML: 0.067 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R Free: 0.08 / 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: 31.095 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.854 Å / Origin y: 58.549 Å / Origin z: 30.333 Å
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