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- PDB-1f7r: CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOS... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1f7r | ||||||
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Title | CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOSPHATASE AND ITS NUCLEOTIDE COMPLEXES IN THREE CRYSTAL FORMS. | ||||||
![]() | POL POLYPROTEIN | ||||||
![]() | Viral protein / hydrolase / Eight stranded beta barrel protein | ||||||
Function / homology | ![]() 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 / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Prasad, G.S. / Stura, E.A. / Elder, J.H. / Stout, C.D. | ||||||
![]() | ![]() 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: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 39.7 KB | Display | ![]() |
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PDB format | ![]() | 27.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 439.3 KB | Display | ![]() |
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Full document | ![]() | 440.9 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 6.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f7dC ![]() 1f7kC ![]() 1f7nC ![]() 1f7oC ![]() 1f7pC ![]() 1f7qC 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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Details | Trimer is the functional form of the enzyme |
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Components
#1: Protein | Mass: 14730.169 Da / Num. of mol.: 1 / Fragment: DUTPASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-UDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.79 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.25 M sodium citrate. The protein solution was incubated with 25 mM dUDP prior to crystallization experiments., 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: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 27, 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: 2.5→50 Å / Num. all: 10960 / Num. obs: 4414 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.246 / % possible all: 92.5 |
Reflection | *PLUS Num. measured all: 10960 |
Reflection shell | *PLUS % possible obs: 92.5 % / Mean I/σ(I) obs: 4.5 |
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Processing
Refinement | Resolution: 2.5→50 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.5→50 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.192 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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