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Yorodumi- PDB-4icl: HIV-1 reverse transcriptase with bound fragment at the incoming d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4icl | ||||||
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Title | HIV-1 reverse transcriptase with bound fragment at the incoming dNTP binding site | ||||||
Components |
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Keywords | transferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / transferase-transferase inhibitor complex | ||||||
Function / homology | Function and homology information 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 ...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 / 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 / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 type 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Bauman, J.D. / Patel, D. / Arnold, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Detecting Allosteric Sites of HIV-1 Reverse Transcriptase by X-ray Crystallographic Fragment Screening. Authors: Bauman, J.D. / Patel, D. / Dharia, C. / Fromer, M.W. / Ahmed, S. / Frenkel, Y. / Vijayan, R.S. / Eck, J.T. / Ho, W.C. / Das, K. / Shatkin, A.J. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4icl.cif.gz | 619.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4icl.ent.gz | 519.9 KB | Display | PDB format |
PDBx/mmJSON format | 4icl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4icl_validation.pdf.gz | 786.7 KB | Display | wwPDB validaton report |
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Full document | 4icl_full_validation.pdf.gz | 808.7 KB | Display | |
Data in XML | 4icl_validation.xml.gz | 44.4 KB | Display | |
Data in CIF | 4icl_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/4icl ftp://data.pdbj.org/pub/pdb/validation_reports/ic/4icl | HTTPS FTP |
-Related structure data
Related structure data | 4id5C 4idkC 4ifvC 4ifyC 4ig0C 4ig3C 4kfbC 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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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 63989.238 Da / Num. of mol.: 1 / Fragment: P66 (unp residues 600-1154) / Mutation: K771A, K772A, C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
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#2: Protein | Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: P51 (unp residues 600-1027) / Mutation: C879S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol, POL / Plasmid: PCDF-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIL) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, retroviral ribonuclease H |
-Non-polymers , 5 types, 703 molecules
#3: Chemical | ChemComp-T27 / | ||||
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#4: Chemical | ChemComp-MG / | ||||
#5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-14N / | #7: 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: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.7 Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE, AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, PH 6.7, VAPOR DIFFUSION, TEMPERATURE 277.0K , VAPOR ...Details: 11% PEG 8000, 4% PEG 400, 50 MM IMIDAZOLE, 10 MM SPERMINE, 15 MM MGSO4, 100 MM AMMONIUM SULFATE, AND 5 MM TRIS(2-CARBOXYETHYL)PHOSPHINE, PH 6.7, VAPOR DIFFUSION, TEMPERATURE 277.0K , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.917 / Wavelength: 0.917 Å | |||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2008 | |||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→50 Å / Num. all: 119988 / Num. obs: 117469 / % possible obs: 97.9 % / Observed criterion σ(F): -2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 21.01 | |||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→38 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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