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Yorodumi- PDB-1yn9: Crystal structure of baculovirus RNA 5'-phosphatase complexed wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yn9 | ||||||
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Title | Crystal structure of baculovirus RNA 5'-phosphatase complexed with phosphate | ||||||
Components | polynucleotide 5'-phosphatase | ||||||
Keywords | HYDROLASE / RNA triphosphatase / cysteine phosphatase / P-loop | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity Similarity search - Function | ||||||
Biological species | Autographa californica nucleopolyhedrovirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Changela, A. / Martins, A. / Shuman, S. / Mondragon, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Crystal structure of baculovirus RNA triphosphatase complexed with phosphate Authors: Changela, A. / Martins, A. / Shuman, S. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yn9.cif.gz | 126.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yn9.ent.gz | 98.2 KB | Display | PDB format |
PDBx/mmJSON format | 1yn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/1yn9 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/1yn9 | HTTPS FTP |
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-Related structure data
Related structure data | 1i9tS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 19450.449 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Autographa californica nucleopolyhedrovirus Genus: NucleopolyhedrovirusAlphabaculovirus / Gene: PTP / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P24656, polynucleotide 5'-phosphatase #2: Chemical | ChemComp-PO4 / #3: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: sodium/potassium phosphate, sodium acetate, guanidine hydrochloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9479 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jan 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9479 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→150 Å / Num. all: 424098 / Num. obs: 97263 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.066 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6308 / Rsym value: 0.25 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1I9T Resolution: 1.5→105.41 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.087 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.068 / Stereochemistry target values: Engh & Huber / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.41 Å2
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Refine analyze | Luzzati coordinate error free: 0.042 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→105.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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