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Yorodumi- PDB-1f7q: CRYSTAL STRUCTURES OF FELINE IMMUNODEFICIENCY VIRUS DUTP PYROPHOS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1f7q | ||||||
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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: 2.26 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 | 1f7q.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1f7q.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 1f7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1f7q_validation.pdf.gz | 523.5 KB | Display | wwPDB validaton report |
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Full document | 1f7q_full_validation.pdf.gz | 538.9 KB | Display | |
Data in XML | 1f7q_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 1f7q_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/1f7q ftp://data.pdbj.org/pub/pdb/validation_reports/f7/1f7q | HTTPS FTP |
-Related structure data
Related structure data | 1f7dC 1f7kC 1f7nC 1f7oC 1f7pC 1f7rC 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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Details | Trimer is the functional form of the enzyme |
-Components
#1: Protein | Mass: 14730.169 Da / Num. of mol.: 3 / 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: 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: 2.13 Å3/Da / Density % sol: 42.27 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.0M Sodium citrate pH 6.5. The crystals were soaked in 10 mM dUDP for 24 hrs, 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: Jan 30, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→30 Å / Num. all: 51135 / Num. obs: 18741 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 2 |
Reflection shell | Resolution: 2.26→2.32 Å / Rmerge(I) obs: 0.459 / % possible all: 93.7 |
Reflection | *PLUS Num. measured all: 51135 |
Reflection shell | *PLUS % possible obs: 93.7 % / Mean I/σ(I) obs: 1.5 |
-Processing
Refinement | Resolution: 2.26→30 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.26→30 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 30 Å / σ(F): 2 / Rfactor Rwork: 0.232 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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