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Yorodumi- PDB-1ed1: CRYSTAL STRUCTURE OF SIMIAN IMMUNODEFICIENCY VIRUS MATRIX ANTIGEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ed1 | ||||||
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Title | CRYSTAL STRUCTURE OF SIMIAN IMMUNODEFICIENCY VIRUS MATRIX ANTIGEN (SIV MA) AT 100K. | ||||||
Components | GAG POLYPROTEINGroup-specific antigen | ||||||
Keywords | VIRAL PROTEIN / Trimeric Association | ||||||
Function / homology | Function and homology information viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency ...viral process / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / host cell cytoplasm / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / host cell nucleus / structural molecule activity / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Simian immunodeficiency virus - mac | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å | ||||||
Authors | Rao, Z. / Belyaev, A. / Fry, E. / Roy, P. / Jones, I.M. / Stuart, D.I. | ||||||
Citation | Journal: Nature / Year: 1995 Title: Crystal structure of SIV matrix antigen and implications for virus assembly. Authors: Rao, Z. / Belyaev, A.S. / Fry, E. / Roy, P. / Jones, I.M. / Stuart, D.I. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystallization and Preliminary X-ray Investigation of Recombinant Simian Immunodeficiency Virus Matrix Antigen Authors: Belyaev, A. / Stuart, D. / Sutton, G. / Roy, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ed1.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ed1.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 1ed1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/1ed1 ftp://data.pdbj.org/pub/pdb/validation_reports/ed/1ed1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly may be represented by the trimeric association of molecules within the crystal. |
-Components
#1: Protein | Mass: 14923.270 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SIV MATRIX ANTIGEN / Source: (gene. exp.) Simian immunodeficiency virus - mac / Genus: Lentivirus / Species: Simian immunodeficiency virus / Strain: MAC BK28 / Gene: GAG / Plasmid: PULB5002 / Production host: unidentified baculovirus / References: UniProt: Q03859, UniProt: P05897*PLUS | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.4 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG 8000, isopropanol, Tris-HCL, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 8719 / Num. obs: 8719 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Num. measured all: 43654 |
-Processing
Software |
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Refinement | Resolution: 2.1→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.4 |