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Yorodumi- PDB-4kfb: HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kfb | |||||||||
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Title | HIV-1 reverse transcriptase with bound fragment at NNRTI adjacent site | |||||||||
Components |
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Keywords | transferase/transferase inhibitor / RNA-DIRECTED DNA POLYMERASE / DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MULTIFUNCTIONAL ENZYME / HYDROLASE-INHIBITOR COMPLEX / 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 / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / 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 TYPE 1 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.854 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 | 4kfb.cif.gz | 428.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kfb.ent.gz | 349.1 KB | Display | PDB format |
PDBx/mmJSON format | 4kfb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kfb_validation.pdf.gz | 784.7 KB | Display | wwPDB validaton report |
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Full document | 4kfb_full_validation.pdf.gz | 798 KB | Display | |
Data in XML | 4kfb_validation.xml.gz | 42.8 KB | Display | |
Data in CIF | 4kfb_validation.cif.gz | 63.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kf/4kfb ftp://data.pdbj.org/pub/pdb/validation_reports/kf/4kfb | HTTPS FTP |
-Related structure data
Related structure data | 4iclC 4id5C 4idkC 4ifvC 4ifyC 4ig0C 4ig3C 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 / Mutation: K172A, K173A, C280S 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, exoribonuclease H |
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#2: Protein | Mass: 50096.539 Da / Num. of mol.: 1 / Fragment: p51 RT / Mutation: C280S 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 |
-Non-polymers , 4 types, 671 molecules
#3: Chemical | ChemComp-1QP / | ||||
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#4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-T27 / | #6: 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: 2.77 Å3/Da / Density % sol: 55.55 % |
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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, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 / Wavelength: 0.917 Å | |||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 2, 2010 | |||||||||
Radiation | Monochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.854→43.297 Å / Num. obs: 105443 / % possible obs: 95.1 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.79 | |||||||||
Reflection shell | Resolution: 1.85→1.88 Å / % possible all: 86.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.854→43.297 Å / SU ML: 0.22 / σ(F): 1.34 / Phase error: 23.02 / 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: 1.854→43.297 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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