[English] 日本語
![](img/lk-miru.gif)
- PDB-1f7d: CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOS... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1f7d | ||||||
---|---|---|---|---|---|---|---|
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 | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 62.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 44.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 380.2 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 10.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1f7kC ![]() 1f7nC ![]() 1f7oC ![]() 1f7pC ![]() 1f7qC ![]() 1f7rC C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||
3 | ![]()
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||
Details | The biological assembly is a trimer |
-
Components
#1: Protein | Mass: 14730.169 Da / Num. of mol.: 2 / Fragment: DUTPASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.89 % | ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 13% MPEG 5K, 50mM Sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→20 Å / Num. all: 212437 / Num. obs: 55495 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 1.4→1.44 Å / Rmerge(I) obs: 0.031 / % possible all: 82.3 |
Reflection | *PLUS Num. measured all: 212437 |
Reflection shell | *PLUS % possible obs: 82.3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.1 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.4→20 Å / σ(F): 2 / σ(I): 4
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 2 / % reflection Rfree: 3 % / Rfactor obs: 0.178 / Rfactor Rwork: 0.179 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|