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Yorodumi- PDB-1axa: ACTIVE-SITE MOBILITY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1axa | |||||||||
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Title | ACTIVE-SITE MOBILITY IN HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 PROTEASE AS DEMONSTRATED BY CRYSTAL STRUCTURE OF A28S MUTANT | |||||||||
Components | HIV-1 PROTEASE | |||||||||
Keywords | ASPARTYL PROTEASE / HIV PROTEASE / MUTANT / ASPARTIC PROTEASE / HYDROLASE / ACID PROTEINASE | |||||||||
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 1 | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2 Å | |||||||||
Authors | Hong, L. / Hartsuck, J.A. / Foundling, S. / Ermolieff, J. / Tang, J. | |||||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Active-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant. Authors: Hong, L. / Hartsuck, J.A. / Foundling, S. / Ermolieff, J. / Tang, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1axa.cif.gz | 54 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1axa.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 1axa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1axa_validation.pdf.gz | 495.3 KB | Display | wwPDB validaton report |
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Full document | 1axa_full_validation.pdf.gz | 505.8 KB | Display | |
Data in XML | 1axa_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 1axa_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axa ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axa | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.49848, -0.8669, 0.00101), Vector: |
-Components
#1: Protein | Mass: 10819.756 Da / Num. of mol.: 2 / Mutation: A28S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03366, 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: 2.2 Å3/Da / Density % sol: 44 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 / Details: pH 6.8 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 5.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1996 |
Radiation | Monochromator: CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→34 Å / Num. obs: 11025 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.064 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2→2.2 Å / Redundancy: 2 % / Mean I/σ(I) obs: 3 / Rsym value: 0.25 / % possible all: 76 |
Reflection | *PLUS Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 75.9 % |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
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Solvent computation | Solvent model: BABINET / Bsol: 266.2 Å2 / ksol: 0.818 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Version: 5E / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.194 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 37.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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