+Open data
-Basic information
Entry | Database: PDB / ID: 2q64 | ||||||
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Title | HIV-1 PR mutant in complex with nelfinavir | ||||||
Components | PROTEASE RETROPEPSIN | ||||||
Keywords | HYDROLASE / resistance / nelfinavir | ||||||
Function / homology | Function and homology information RNA stem-loop binding / host cell / 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 ...RNA stem-loop binding / host cell / 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 / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rezacova, P. / Kozisek, M. / Saskova, K. / Brynda, J. / Konvalinka, J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Molecular analysis of the HIV-1 resistance development: enzymatic activities, crystal structures, and thermodynamics of nelfinavir-resistant HIV protease mutants Authors: Kozisek, M. / Bray, J. / Rezacova, P. / Saskova, K. / Brynda, J. / Pokorna, J. / Mammano, F. / Rulisek, L. / Konvalinka, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q64.cif.gz | 55.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q64.ent.gz | 39.8 KB | Display | PDB format |
PDBx/mmJSON format | 2q64.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/2q64 ftp://data.pdbj.org/pub/pdb/validation_reports/q6/2q64 | HTTPS FTP |
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-Related structure data
Related structure data | 2pymC 2pynC 2q63C 1u8gS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 2
NCS ensembles :
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Details | the biological assembly is dimer |
-Components
#1: Protein | Mass: 10716.655 Da / Num. of mol.: 2 / Mutation: D30N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: type B / Gene: gag-pol / Plasmid: pET like, T7 promotor driven / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P03367, HIV-1 retropepsin #2: Chemical | ChemComp-1UN / | #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: 42.46 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.98 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 2, 2005 / Details: double crystal monochromator |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 6313 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 49.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1U8G Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.879 / SU B: 22.529 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.728 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.565 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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