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Yorodumi- PDB-2xde: Crystal structure of the complex of PF-3450074 with an engineered... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xde | |||||||||
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Title | Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal domain | |||||||||
Components | GAG POLYPROTEIN | |||||||||
Keywords | VIRAL PROTEIN / AIDS | |||||||||
Function / homology | Function and homology information viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...viral process / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / viral capsid / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | |||||||||
Biological species | HUMAN IMMUNODEFICIENCY VIRUS 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | |||||||||
Authors | Brown, D.G. / Irving, S.L. / Anderson, M. / Bazin, R. | |||||||||
Citation | Journal: Plos Pathog. / Year: 2010 Title: HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention. Authors: Blair, W.S. / Pickford, C. / Irving, S.L. / Brown, D.G. / Anderson, M. / Bazin, R. / Cao, J. / Ciaramella, G. / Isaacson, J. / Jackson, L. / Hunt, R. / Kjerrstrom, A. / Nieman, J. / Patick, ...Authors: Blair, W.S. / Pickford, C. / Irving, S.L. / Brown, D.G. / Anderson, M. / Bazin, R. / Cao, J. / Ciaramella, G. / Isaacson, J. / Jackson, L. / Hunt, R. / Kjerrstrom, A. / Nieman, J. / Patick, A.K. / Perros, M. / Scott, A.D. / Whitby, K. / Wu, H. / Butler, S.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xde.cif.gz | 76 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xde.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 2xde.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xde_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2xde_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2xde_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2xde_validation.cif.gz | 25.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/2xde ftp://data.pdbj.org/pub/pdb/validation_reports/xd/2xde | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.99996, 0.00158, 0.00824), Vector: |
-Components
#1: Protein | Mass: 16217.491 Da / Num. of mol.: 2 / Fragment: N TERMINAL DOMAIN, RESIDUES 1-146 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Strain: NL4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9IQV5, UniProt: P12497*PLUS #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: 1.8 Å3/Da / Density % sol: 31.78 % / Description: NONE |
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Crystal grow | pH: 8 Details: 2ULOF PROTEIN (30MG/ML)AND 2UL OF WELL SOLUTION (20% PEG 8000, 100 MM PHOSPHATE-CITRATE PH 4.2 AND 200 MM SODIUM CHLORIDE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 20, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. obs: 44735 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: TRUNCATED MODEL OF N TERMINAL CAPSID Resolution: 1.4→20.72 Å / Cor.coef. Fo:Fc: 0.962 / SU B: 1.176 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.093 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→20.72 Å
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