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Yorodumi- PDB-3trl: Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3trl | ||||||
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Title | Crystal structure of M-PMV dUTPASE post-inversion product (dUMP) complex | ||||||
Components | DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDO HYDROLASE | ||||||
Keywords | HYDROLASE / jelly roll | ||||||
Function / homology | Function and homology information 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 | Mason-pfizer monkey virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.8 Å | ||||||
Authors | Barabas, O. / Nemeth, V. / Vertessy, B.G. | ||||||
Citation | Journal: To be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3trl.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3trl.ent.gz | 44.9 KB | Display | PDB format |
PDBx/mmJSON format | 3trl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tr/3trl ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3trl | HTTPS FTP |
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-Related structure data
Related structure data | 3tp1C 3tpnC 3tpsC 3tpwC 3tpyC 3tq3C 3tq4C 3tq5C 2d4lS 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: 16155.373 Da / Num. of mol.: 1 / Fragment: dUTPase (catalytic) domain, UNP RESIDUES 608-759 / Mutation: N1K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mason-pfizer monkey virus / Gene: gag-pro / Plasmid: pET22B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O92810, UniProt: P07570*PLUS, dUTP diphosphatase |
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#2: Chemical | ChemComp-UMP / |
#3: 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: 2.12 Å3/Da / Density % sol: 41.86 % |
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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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8128 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2004 / Details: mirrors |
Radiation | Monochromator: Si [111], horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8128 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. all: 12312 / Num. obs: 12312 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Rsym value: 0.063 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 1861 / Rsym value: 0.463 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: rigid body refinement Starting model: PDB ENTRY 2D4L Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.96 / SU B: 5.596 / SU ML: 0.081 / Isotropic thermal model: TLS and isotropic individual / Cross valid method: THROUGHOUT / ESU R Free: 0.099 / 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: 33.508 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 2.8433 Å / Origin y: 58.7935 Å / Origin z: 30.3424 Å
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Refinement TLS group |
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