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Yorodumi- PDB-1lvm: CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lvm | ||||||
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Title | CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH PRODUCT | ||||||
Components |
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Keywords | VIRAL PROTEIN / Beta Barrel / Chymotrypsin-type Cystein Protease / Enzyme-peptide Complex | ||||||
Function / homology | Function and homology information nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / Hydrolases; Acting on peptide bonds (peptidases) / helical viral capsid / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Tobacco etch virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Phan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structural basis for the substrate specificity of tobacco etch virus protease. Authors: Phan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR STATES RESIDUES 308-310 ARE NOT IN THE CRYSTAL OF CHAINS C AND D AND RESIDUES 309- ...SEQUENCE AUTHOR STATES RESIDUES 308-310 ARE NOT IN THE CRYSTAL OF CHAINS C AND D AND RESIDUES 309-310 ARE NOT IN THE PEPTIDE SEQUENCE FOR THIS MUTANT. RESIDUE GLY 308 WAS CLEAVED OFF BY THE ENZYME AND NOT PRESENT IN THE CRYSTAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lvm.cif.gz | 116.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lvm.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 1lvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/1lvm ftp://data.pdbj.org/pub/pdb/validation_reports/lv/1lvm | HTTPS FTP |
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-Related structure data
Related structure data | 1lvbSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26147.586 Da / Num. of mol.: 2 / Fragment: Residues 1-221 / Mutation: S219D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517 #2: Protein/peptide | Mass: 1084.137 Da / Num. of mol.: 2 / Fragment: Residues 302-310 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517 #3: Protein/peptide | | Mass: 805.896 Da / Num. of mol.: 1 / Fragment: Residues 230-236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: BL21(DE3) / Production host: Escherichia coli (E. coli) / Strain (production host): pRK529 / References: UniProt: P04517 #4: 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: 2.36 Å3/Da / Density % sol: 47.9 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulfate, magnesium chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 18, 2001 / Details: Mirrors |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 49988 / Num. obs: 48452 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.058 |
Reflection shell | Resolution: 1.8→1.86 Å / % possible all: 99.3 |
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. obs: 49988 / % possible obs: 99.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LVB Resolution: 1.8→25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 140622.42 / Data cutoff high rms absF: 140622.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 54.5232 Å2 / ksol: 0.334191 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. reflection obs: 43567 / Rfactor Rfree: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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