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Yorodumi- PDB-3klf: Crystal structure of wild-type HIV-1 Reverse Transcriptase crossl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3klf | ||||||
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Title | Crystal structure of wild-type HIV-1 Reverse Transcriptase crosslinked to a DSDNA with a bound excision product, AZTPPPPA | ||||||
Components |
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Keywords | TRANSFERASE/DNA / AZT RESISTANCE MECHANISM / HIV-1 REVERSE TRANSCRIPTASE / WILD-TYPE / AZT RESISTANCE MUTATIONS / P51/P66 / NUCELEOSIDE INHIBITOR / THYMIDINE ANALOG MUTATIONS / AIDS / HIV / DNA POLYMERASE / NRTI / NRTI RESISTANCE / AZT / AZTPPPPA / AZTP4A / DINUCLEOSIDE TETRAPHOSPHATE / DNA-DIRECTED DNA POLYMERASE / ENDONUCLEASE / HYDROLASE / MAGNESIUM / METAL-BINDING / MULTIFUNCTIONAL ENZYME / NUCLEASE / RNA-DIRECTED DNA POLYMERASE / TRANSFERASE / TRANSFERASE-DNA 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: 3.15 Å | ||||||
Authors | Tu, X. / Das, K. / Sarafianos, S.G. / Arnold, E. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2010 Title: Structural basis of HIV-1 resistance to AZT by excision. Authors: Tu, X. / Das, K. / Han, Q. / Bauman, J.D. / Clark, A.D. / Hou, X. / Frenkel, Y.V. / Gaffney, B.L. / Jones, R.A. / Boyer, P.L. / Hughes, S.H. / Sarafianos, S.G. / Arnold, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3klf.cif.gz | 883.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3klf.ent.gz | 710.2 KB | Display | PDB format |
PDBx/mmJSON format | 3klf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3klf_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3klf_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3klf_validation.xml.gz | 103.8 KB | Display | |
Data in CIF | 3klf_validation.cif.gz | 150.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kl/3klf ftp://data.pdbj.org/pub/pdb/validation_reports/kl/3klf | HTTPS FTP |
-Related structure data
Related structure data | 3kleC 3klgC 3klhC 3kliC 1rtdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 2 types, 8 molecules AEIMBFJN
#1: Protein | Mass: 64080.457 Da / Num. of mol.: 4 / Mutation: C280S, Q258C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Plasmid: PRT35A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P03366, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H #2: Protein | Mass: 51928.629 Da / Num. of mol.: 4 / Mutation: C280S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BH10 / Gene: gag-pol / Plasmid: PRT35A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03366 |
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-DNA chain , 2 types, 8 molecules CGKODHLP
#3: DNA chain | Mass: 8367.386 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA TEMPLATE FOR REVERSE TRANSCRIPTASE #4: DNA chain | Mass: 6458.268 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: DNA PRIMER FOR REVERSE TRANSCRIPTASE |
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-Non-polymers , 4 types, 90 molecules
#5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-ZP4 / [[[[( #7: Chemical | #8: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 3.14 Å3/Da / Density % sol: 60.85 % |
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Crystal grow | pH: 6.8 Details: 50 MM BIS-TRIS PROPANE PH6.4, 10-11% PEG8000, 0.3 M (NH4)2SO4, 5% GLYCEROL, 5% SUCROSE, 20 MM MGCL2, AND 5 MM SPERMIDINE, PH 6.8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.15→25 Å / Num. obs: 98589 / % possible obs: 90.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.129 |
Reflection shell | Resolution: 3.15→3.21 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.539 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RTD Resolution: 3.15→24.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4028470 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.82 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.15→24.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.15→3.35 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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