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Yorodumi- PDB-3iaw: Crystal structure of a chemically synthesized 203 amino acid 'cov... -
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-Basic information
Entry | Database: PDB / ID: 3iaw | ||||||
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Title | Crystal structure of a chemically synthesized 203 amino acid 'covalent dimer' [Gly51;Aib51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor at 1.6 A resolution | ||||||
Components | [Gly51;Aib51'] 'covalent dimer' HIV-1 protease | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / asymmetric dimer / covalent dimer / beta-sheet / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 | 3iaw.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iaw.ent.gz | 43.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iaw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ia/3iaw ftp://data.pdbj.org/pub/pdb/validation_reports/ia/3iaw | HTTPS FTP |
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-Related structure data
Related structure data | 3fsmC 3hauC 3hawC 3hboC 3hdkC 3hloC 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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1 |
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Unit cell |
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-Components
#1: Protein | [ Mass: 21919.703 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: total chemical synthesis / References: UniProt: P03369*PLUS, HIV-1 retropepsin |
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#2: Chemical | ChemComp-2NC / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.08 Å3/Da / Density % sol: 40.91 % |
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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% (w/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: 23-ID-D / Wavelength: 0.97932 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2006 Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geomet ry |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97932 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 24056 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 39 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 7 % / Rmerge(I) obs: 0.514 / Mean I/σ(I) obs: 6.2 / Num. unique all: 2425 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.727 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.104 / 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: 23.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.61→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.605→1.647 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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