+Open data
-Basic information
Entry | Database: PDB / ID: 1n80 | ||||||
---|---|---|---|---|---|---|---|
Title | Bacteriophage T4 baseplate structural protein gp8 | ||||||
Components | baseplate structural protein gp8 | ||||||
Keywords | VIRAL PROTEIN / bacteriophage T4 / baseplate / dimer / beta sandwich / halide binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Leiman, P.G. / Shneider, M.M. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structure and location of gene product 8 in the bacteriophage T4 baseplate Authors: Leiman, P.G. / Shneider, M.M. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Rossmann, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1n80.cif.gz | 277.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1n80.ent.gz | 225.7 KB | Display | PDB format |
PDBx/mmJSON format | 1n80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n80_validation.pdf.gz | 463.5 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1n80_full_validation.pdf.gz | 516.9 KB | Display | |
Data in XML | 1n80_validation.xml.gz | 57.4 KB | Display | |
Data in CIF | 1n80_validation.cif.gz | 79.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/1n80 ftp://data.pdbj.org/pub/pdb/validation_reports/n8/1n80 | HTTPS FTP |
-Related structure data
Related structure data | 1n7zSC 1n8bC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
| ||||||||
Details | the asymmetric unit contains two biologically active identical dimers |
-Components
#1: Protein | Mass: 38041.668 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: gene 8 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19062 #2: Chemical | ChemComp-CL / #3: Water | ChemComp-HOH / | Has protein modification | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 46.77 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: HEPES, PEG 6000, LiCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.0723 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2000 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 51148 / Num. obs: 49960 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 9.1 / Num. unique all: 2133 / % possible all: 82.4 |
Reflection | *PLUS Lowest resolution: 50 Å |
Reflection shell | *PLUS % possible obs: 82.4 % / Redundancy: 2.9 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N7Z Resolution: 2.45→39.11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1056545.54 / Data cutoff high rms absF: 1056545.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 46.1366 Å2 / ksol: 0.342653 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.4 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→39.11 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.45→2.56 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|