+Open data
-Basic information
Entry | Database: PDB / ID: 5fgy | ||||||
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Title | Structure of human adenovirus 2 protease with cofactor pVIC | ||||||
Components |
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Keywords | HYDROLASE / protease / cofactor / complex | ||||||
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 cytoplasm ...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 cytoplasm / cysteine-type endopeptidase activity / host cell nucleus / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human adenovirus C serotype 2 Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Davis, R.R. / Martinez, P. / Hollis, T. | ||||||
Citation | Journal: To Be Published Title: Structure of human adenovirus 2 protease with cofactor pVIC Authors: Davis, R.R. / Martinez, P. / Hollis, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fgy.cif.gz | 101.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fgy.ent.gz | 77.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/5fgy ftp://data.pdbj.org/pub/pdb/validation_reports/fg/5fgy | HTTPS FTP |
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-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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human adenovirus C serotype 2 / Gene: L3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03252, adenain |
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#2: Protein/peptide | Mass: 1353.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P03274*PLUS |
#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: 3.71 Å3/Da / Density % sol: 66.85 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.4 Details: Grew over one week at 4 degrees Celsius in 0.1 M sodium citrate pH 6.4, 1.7 M sodium acetate, 1 mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 70 / Detector: CCD / Date: Nov 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→97.36 Å / Num. obs: 20733 / % possible obs: 97.7 % / Redundancy: 5.54 % / Rmerge(I) obs: 0.059 / Rsym value: 0.065 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 4.46 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 6 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AVP Resolution: 2.1→97.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.185 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.214 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→97.36 Å
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Refine LS restraints |
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