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Yorodumi- PDB-6o54: Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o54 | ||||||
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Title | Crystal Structure of multi-drug resistant HIV-1 protease PR-S17 (D25N) | ||||||
Components | HIV-1 protease | ||||||
Keywords | HYDROLASE / Viral Protein / HIV PROTEASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Wang, Y.-F. / Brothers, R. / Agniswamy, J. / Weber, I.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Omega / Year: 2019 Title: Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues. Authors: Agniswamy, J. / Kneller, D.W. / Brothers, R. / Wang, Y.F. / Harrison, R.W. / Weber, I.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6o54.cif.gz | 60.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o54.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 6o54.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/6o54 ftp://data.pdbj.org/pub/pdb/validation_reports/o5/6o54 | HTTPS FTP |
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-Related structure data
Related structure data | 6o48C 6o57C 6o5aC 6o5xC 5t2eS S: Starting model for refinement 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 10790.608 Da / Num. of mol.: 1 / Mutation: D25N, M46L, G48V, C67A, V77I, A82S, I93L, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7BFC3 | ||
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#2: Chemical | ChemComp-CL / #3: 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: 2.86 Å3/Da / Density % sol: 56.97 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.95 M sodium chloride, 0.1 M Bis-Tris, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Feb 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→50 Å / Num. obs: 35459 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.035 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.21→1.25 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2 / Num. unique obs: 1956 / CC1/2: 0.751 / Rpim(I) all: 0.318 / Χ2: 1.004 / % possible all: 52.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5T2E Resolution: 1.21→38.55 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.06 / SU ML: 0.021 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.034 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.01 Å2
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Refinement step | Cycle: 1 / Resolution: 1.21→38.55 Å
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Refine LS restraints |
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