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Yorodumi- PDB-3liy: crystal structure of HTLV protease complexed with Statine-contain... -
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-Basic information
Entry | Database: PDB / ID: 3liy | ||||||
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Title | crystal structure of HTLV protease complexed with Statine-containing peptide inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / Statine / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Human T-lymphotropic virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.86 Å | ||||||
Authors | Satoh, T. / Li, M. / Nguyen, J. / Kiso, Y. / Wlodawer, A. / Gustchina, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structures of inhibitor complexes of human T-cell leukemia virus (HTLV-1) protease. Authors: Satoh, T. / Li, M. / Nguyen, J.T. / Kiso, Y. / Gustchina, A. / Wlodawer, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3liy.cif.gz | 288.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3liy.ent.gz | 238.3 KB | Display | PDB format |
PDBx/mmJSON format | 3liy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/li/3liy ftp://data.pdbj.org/pub/pdb/validation_reports/li/3liy | HTTPS FTP |
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-Related structure data
Related structure data | 3linC 3liqC 3litC 3livC 3lixC 2b7fS 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 12566.579 Da / Num. of mol.: 6 / Mutation: L40I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Gene: prt / Plasmid: pHTLVdelta9 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: Q82134 #2: Protein/peptide | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THE INHIBITOR IS OBTAINED FROM ASSOCIATED | |
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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: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 17% PEG8000, 16% PEG300 and 10mM DTT, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→50 Å / Num. obs: 66670 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.053 / Net I/σ(I): 22.1 |
Reflection shell | Resolution: 1.86→1.96 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 5985 / Rsym value: 0.449 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 2B7F Resolution: 1.86→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.072 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.127 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.926 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.861→1.909 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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