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Yorodumi- PDB-3hdk: Crystal structure of chemically synthesized [Aib51/51']HIV-1 protease -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdk | ||||||
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Title | Crystal structure of chemically synthesized [Aib51/51']HIV-1 protease | ||||||
Components | [Aib51/51']HIV-1 protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / beta barrel / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / 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 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Torbeev, V.Y. / Kent, S.B.H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2011 Title: Protein conformational dynamics in the mechanism of HIV-1 protease catalysis. Authors: Torbeev, V.Y. / Raghuraman, H. / Hamelberg, D. / Tonelli, M. / Westler, W.M. / Perozo, E. / Kent, S.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hdk.cif.gz | 50.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdk.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hdk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hdk_validation.pdf.gz | 722.9 KB | Display | wwPDB validaton report |
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Full document | 3hdk_full_validation.pdf.gz | 725.8 KB | Display | |
Data in XML | 3hdk_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 3hdk_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdk ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdk | HTTPS FTP |
-Related structure data
Related structure data | 3fsmC 3hauC 3hawC 3hboC 3hloC 3iawC 3ka2C 3nwqC 3nwxC 3nxeC 3nxnC 3nygC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | 1 |
-Components
#1: Protein | Mass: 10745.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Total chemical synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin #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: 2.14 Å3/Da / Density % sol: 42.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 0.1 M citrate, 0.2 M sodium phosphate, 30% (v/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97985 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2006 Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal f ocusing. Rosenbaum-Rock vertical focusing mirror. |
Radiation | Monochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97985 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 17740 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 3.49 / Num. unique all: 1709 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.404 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.128 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.985 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.796→1.842 Å / Total num. of bins used: 20
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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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