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Yorodumi- PDB-1nln: CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AM... -
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-Basic information
Entry | Database: PDB / ID: 1nln | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN ADENOVIRUS 2 PROTEINASE WITH ITS 11 AMINO ACID COFACTOR AT 1.6 ANGSTROM RESOLUTION | ||||||
Components |
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Keywords | HYDROLASE / THIOL HYDROLASE / VIRAL PROTEINASE / PEPTIDE COFACTOR | ||||||
Function / homology | Function and homology information nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell ...nuclear capsid assembly / adenain / lysis of host organelle involved in viral entry into host cell / viral procapsid / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / cysteine-type peptidase activity / virion component / viral capsid / host cell / host cell cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human adenovirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | McGrath, W.J. / Ding, J. / Sweet, R.M. / Mangel, W.F. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2003 Title: Crystallographic structure at 1.6-A resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor: insights on a new fold Authors: McGrath, W.J. / Ding, J. / Didwania, A. / Sweet, R.M. / Mangel, W.F. #1: Journal: Embo J. / Year: 1996 Title: Crystal Structure of the Human Adenovirus Proteinase with its 11 Amino-acid Cofactor Authors: Ding, J. / McGrath, W.J. / Sweet, R.M. / Mangel, W.F. #2: Journal: J.Biol.Chem. / Year: 1996 Title: Characterization of Three Components of Human Adenovirus Proteinase Activity in vitro #3: Journal: Nature / Year: 1993 Title: Viral DNA and a Viral Peptide can act as Cofactors of Adenovirus Virion Proteinase Activity | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nln.cif.gz | 62.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nln.ent.gz | 44.7 KB | Display | PDB format |
PDBx/mmJSON format | 1nln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nln_validation.pdf.gz | 452.3 KB | Display | wwPDB validaton report |
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Full document | 1nln_full_validation.pdf.gz | 456.8 KB | Display | |
Data in XML | 1nln_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 1nln_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nl/1nln ftp://data.pdbj.org/pub/pdb/validation_reports/nl/1nln | HTTPS FTP |
-Related structure data
Related structure data | 1avpS 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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Unit cell |
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-Components
#1: Protein | Mass: 23114.350 Da / Num. of mol.: 1 / Fragment: adenovirus proteinase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / Gene: L3-23k / Plasmid: pET13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03252, adenain |
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#2: Protein/peptide | Mass: 1353.640 Da / Num. of mol.: 1 / Fragment: pvic peptide / Source method: obtained synthetically Details: chemically synthesized C-terminal 11 amino acids from human adenovirus serotype 2 pVI molecule References: UniProt: P03274*PLUS |
#3: Chemical | ChemComp-ACY / |
#4: 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: 3.73 Å3/Da / Density % sol: 67.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: cacodylate, sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal grow | *PLUS Details: McGrath, W.J., (1996) J. Struct. Biol., 117, 77. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Aug 10, 1995 / Details: collimator |
Radiation | Monochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→30 Å / Num. obs: 44449 / % possible obs: 92.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 30.6 |
Reflection shell | Resolution: 1.6→50 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 7.7 / Num. unique all: 3674 / Rsym value: 0.154 / % possible all: 77.1 |
Reflection | *PLUS Num. obs: 44447 / Num. measured all: 166648 |
Reflection shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å / % possible obs: 77.1 % / Mean I/σ(I) obs: 7.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1AVP Resolution: 1.6→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 14.1 Å2 | ||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 1.66 Å |