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Yorodumi- PDB-2b7f: Crystal structure of human T-cell leukemia virus protease, a nove... -
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-Basic information
Entry | Database: PDB / ID: 2b7f | ||||||
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Title | Crystal structure of human T-cell leukemia virus protease, a novel target for anti-cancer design | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host translation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity ...symbiont-mediated suppression of host translation / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / aspartic-type endopeptidase activity / DNA recombination / nucleic acid binding / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont entry into host cell / structural molecule activity / proteolysis / DNA binding / zinc ion binding Similarity search - Function | ||||||
Biological species | Human T-lymphotropic virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Li, M. / Laco, G.S. / Jaskolski, M. / Rozycki, J. / Alexandratos, J. / Wlodawer, A. / Gustchina, A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005 Title: Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design Authors: Li, M. / Laco, G.S. / Jaskolski, M. / Rozycki, J. / Alexandratos, J. / Wlodawer, A. / Gustchina, A. | ||||||
History |
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Remark 7 | NCS RESTRAINTS STATISTICS FOR CONFORMATION B OF CHAIN J NCS RESTRAINTS STATISTICS NCS GROUP NUMBER : ...NCS RESTRAINTS STATISTICS FOR CONFORMATION B OF CHAIN J NCS RESTRAINTS STATISTICS NCS GROUP NUMBER : 3 CHAIN NAMES : I J K NUMBER OF COMPONENTS NCS GROUP : 1 COMPONENT C SSSEQI TO C SSSEQI CODE 1 I 401 I 410 1 1 J 401 J 410 1 1 K 401 K 410 1 GROUP CHAIN COUNT RMS WEIGHT TIGHT POSITIONAL 3 I (A): 67 ; 0.08 ; 0.05 TIGHT POSITIONAL 3 J (A): 67 ; 0.06 ; 0.05 TIGHT POSITIONAL 3 K (A): 67 ; 0.06 ; 0.05 TIGHT THERMAL 3 I (A**2): 67 ; 0.21 ; 0.50 TIGHT THERMAL 3 J (A**2): 67 ; 0.17 ; 0.50 TIGHT THERMAL 3 K (A**2): 67 ; 0.18 ; 0.50 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2b7f.cif.gz | 153.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2b7f.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 2b7f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2b7f_validation.pdf.gz | 514 KB | Display | wwPDB validaton report |
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Full document | 2b7f_full_validation.pdf.gz | 541.9 KB | Display | |
Data in XML | 2b7f_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 2b7f_validation.cif.gz | 44.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/2b7f ftp://data.pdbj.org/pub/pdb/validation_reports/b7/2b7f | HTTPS FTP |
-Related structure data
Related structure data | 1nh0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: PRO / End label comp-ID: PRO
NCS ensembles :
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-Components
#1: Protein | Mass: 12566.579 Da / Num. of mol.: 6 / Fragment: HTLV Protease Delta-9 (residues 33-148) / Mutation: L40I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human T-lymphotropic virus 1 / Genus: Deltaretrovirus / Species: Primate T-lymphotropic virus 1 / Plasmid: pET-21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P10274, UniProt: P03362*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases #2: Protein/peptide | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | THE PEPTIDE INHIBITOR WAS SYNTHESIZED ON AN ABI 431 PEPTIDE SYNTHESIZER (0.25 MM SCALE) STARTING ...THE PEPTIDE INHIBITOR WAS SYNTHESIZE | |
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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: 2.8 Å3/Da / Density % sol: 54.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: PEG8000, PEG300, DTT and Sodium Acetate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-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 225 mm CCD / Detector: CCD / Date: Jul 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 24654 / Num. obs: 24654 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.55 % / Rsym value: 0.089 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 2.6→2.63 Å / Redundancy: 3.53 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2127 / Rsym value: 0.304 / % possible all: 85.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HIVPR, pdb entry 1nh0 Resolution: 2.6→10 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.884 / SU B: 11.634 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS RESTRAINTS STATISTICS reported in remark 3 corresponds to conformation A of chain J in the coordinates. NCS RESTRAINTS STATISTICS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS RESTRAINTS STATISTICS reported in remark 3 corresponds to conformation A of chain J in the coordinates. NCS RESTRAINTS STATISTICS reported in remark 7 corresponds to conformation B of chain J in the coordinates.
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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: 36.364 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→10 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: 2.601→2.664 Å / Total num. of bins used: 20
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