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Yorodumi- PDB-1f7n: CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f7n | ||||||
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Title | CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS. | ||||||
Components | POL POLYPROTEIN | ||||||
Keywords | Viral protein / hydrolase / Eight stranded beta barrel protein | ||||||
Function / homology | Function and homology information dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / aspartic-type endopeptidase activity / DNA recombination / Hydrolases; Acting on ester bonds / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Feline immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Prasad, G.S. / Stura, E.A. / Elder, J.H. / Stout, C.D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structures of feline immunodeficiency virus dUTP pyrophosphatase and its nucleotide complexes in three crystal forms. Authors: Prasad, G.S. / Stura, E.A. / Elder, J.H. / Stout, C.D. #1: Journal: Protein Sci. / Year: 1996 Title: Crystal Structure of dUTP Pyrophosphatase from Feline Immunodeficiency Virus Authors: Prasad, G.S. / Stura, E.A. / McRee, D.E. / Laco, G.S. / Hasselkus-Light, C. / Elder, J.H. / Stout, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1f7n.cif.gz | 61.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f7n.ent.gz | 44 KB | Display | PDB format |
PDBx/mmJSON format | 1f7n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f7n_validation.pdf.gz | 487.3 KB | Display | wwPDB validaton report |
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Full document | 1f7n_full_validation.pdf.gz | 499.6 KB | Display | |
Data in XML | 1f7n_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 1f7n_validation.cif.gz | 11.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f7n ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f7n | HTTPS FTP |
-Related structure data
Related structure data | 1f7dC 1f7kC 1f7oC 1f7pC 1f7qC 1f7rC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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Details | Trimer is the functional form of the enzyme |
-Components
#1: Protein | Mass: 14730.169 Da / Num. of mol.: 2 / Fragment: DUTPASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Feline immunodeficiency virus / Genus: Lentivirus / Plasmid: FIV-34TF10 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P16088, dUTP diphosphatase #2: Chemical | #3: Chemical | #4: 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: 2.67 Å3/Da / Density % sol: 54.01 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13% MPEG 5K, 50 mM Cacodylate. The crystals were soaked in 10 mM dUTP for 24 hrs, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 18, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 88228 / Num. obs: 15858 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.027 / % possible all: 58.1 |
Reflection | *PLUS Num. measured all: 88228 |
Reflection shell | *PLUS % possible obs: 58.1 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.6 |
-Processing
Software |
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Refinement | Resolution: 2.2→50 Å / σ(F): 2 / σ(I): 0 /
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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