+Open data
-Basic information
Entry | Database: PDB / ID: 1ytj | ||||||
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Title | SIV PROTEASE CRYSTALLIZED WITH PEPTIDE PRODUCT | ||||||
Components |
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Keywords | HYDROLASE/PEPTIDE / AIDS / POLYPROTEIN / HYDROLASE / ASPARTYL PROTEASE / ENDONUCLEASE / RNA-DIRECTED DNA POLYMERASE / HYDROLASE-PEPTIDE COMPLEX | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus ...HIV-1 retropepsin / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / host cell cytoplasm / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Simian immunodeficiency virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Three-dimensional structures of HIV-1 and SIV protease product complexes. Authors: Rose, R.B. / Craik, C.S. / Douglas, N.L. / Stroud, R.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ytj.cif.gz | 29.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ytj.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ytj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ytj_validation.pdf.gz | 427.9 KB | Display | wwPDB validaton report |
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Full document | 1ytj_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 1ytj_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | 1ytj_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/1ytj ftp://data.pdbj.org/pub/pdb/validation_reports/yt/1ytj | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 10768.428 Da / Num. of mol.: 1 / Mutation: CHAIN A, S4H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Simian immunodeficiency virus / Genus: Lentivirus / Strain: X90 / Gene: SIV(MAC)239 / Plasmid: PSOD/PR179 / Gene (production host): SIV(MAC)239 / Production host: PTAC-TAC / References: UniProt: P05896, HIV-1 retropepsin |
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#2: Protein/peptide | Mass: 610.614 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 40 % | |||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 3500 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.079 |
Reflection | *PLUS Highest resolution: 2.5 Å |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Software |
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Refinement | Resolution: 2.5→7 Å / σ(F): 0 Details: DENSITY FOR NLE 107 AND SER 108 WAS NOT VISIBLE SO THE AUTHORS ARBITRARILY CHOOSE ONE ATOM OF THE TWO TERMINAL ATOMS TO BE O OF NLE 107 AND THE OTHER TO BE N OF SER 108.
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Displacement parameters | Biso mean: 14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_dihedral_angle_deg / Dev ideal: 26.7 |