+Open data
-Basic information
Entry | Database: PDB / ID: 1p2z | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Refinement of Adenovirus Type 2 Hexon with CNS | |||||||||
Components | Hexon protein | |||||||||
Keywords | VIRAL PROTEIN / ADENOVIRUS / TYPE 2 / HEXON / VIRUS / JELLYROLL / COAT PROTEIN | |||||||||
Function / homology | Function and homology information T=25 icosahedral viral capsid / microtubule-dependent intracellular transport of viral material towards nucleus / symbiont entry into host cell / host cell nucleus / structural molecule activity Similarity search - Function | |||||||||
Biological species | Human adenovirus 2 | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Rux, J.J. / Kuser, P.R. / Burnett, R.M. | |||||||||
Citation | Journal: J.VIROL. / Year: 2003 Title: Structural and phylogenetic analysis of adenovirus hexons by use of high-resolution x-ray crystallographic, molecular modeling, and sequence-based methods Authors: Rux, J.J. / Kuser, P.R. / Burnett, R.M. #1: Journal: MOL.THER. / Year: 2000 Title: Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon. Authors: Rux, J.J. / Burnett, R.M. #2: Journal: J.Mol.Biol. / Year: 1994 Title: The refined crystal structure of hexon, the major coat protein of adenovirus type 2, at 2.9 A resolution. Authors: Athappilly, F.K. / Murali, R. / Rux, J.J. / Cai, Z. / Burnett, R.M. #3: Journal: ADENOVIRUS METHODS AND PROTOCOLS (IN: METHODS IN MOLECULAR MEDICINE, V.21) Year: 1999 Title: Large-scale purification and crystallization of adenovirus hexon Authors: Rux, J.J. / Pascolini, D. / Burnett, R.M. | |||||||||
History |
| |||||||||
Remark 999 | SEQUENCE THE PROTEIN IS ACETYLATED AT THE N-TERMINUS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1p2z.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1p2z.ent.gz | 153.6 KB | Display | PDB format |
PDBx/mmJSON format | 1p2z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2z ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2z | HTTPS FTP |
---|
-Related structure data
Related structure data | 1p30C 1rux C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
| |||||||||
Details | The biological assembly is a trimer generated by the operations z, x, y and y, z, x. |
-Components
#1: Protein | Mass: 109121.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human adenovirus 2 / Genus: Mastadenovirus / Species: Human adenovirus C / References: UniProt: P03277 | ||
---|---|---|---|
#2: Chemical | ChemComp-CIT / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 3.2 Details: 0.5 M SODIUM CITRATE , pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Apr 1, 1991 / Details: MIRRORS |
Radiation | Monochromator: double-mirror focusing system (Supper) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→10 Å / Num. all: 57118 / Num. obs: 48199 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 5.6 Å2 / Rsym value: 0.098 |
Reflection shell | Resolution: 2.2→2.32 Å / Num. unique all: 7162 / % possible all: 75.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RUX 1rux Resolution: 2.2→9.99 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.9291 Å2 / ksol: 0.399606 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→9.99 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
|