+Open data
-Basic information
Entry | Database: PDB / ID: 4zku | ||||||
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Title | P22 Tail Needle Gp26 crystallized at pH 10.0 | ||||||
Components | Tail needle protein gp26 | ||||||
Keywords | VIRAL PROTEIN / P22 / Tail Needle / Membrane penetration | ||||||
Function / homology | Function and homology information symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane Similarity search - Function | ||||||
Biological species | Enterobacteria phage P22 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sankhala, R.S. / Cingolani, G. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Plasticity of the Protein Plug That Traps Newly Packaged Genomes in Podoviridae Virions. Authors: Bhardwaj, A. / Sankhala, R.S. / Olia, A.S. / Brooke, D. / Casjens, S.R. / Taylor, D.J. / Prevelige, P.E. / Cingolani, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zku.cif.gz | 92.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zku.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zku.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zku_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 4zku_full_validation.pdf.gz | 425.6 KB | Display | |
Data in XML | 4zku_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 4zku_validation.cif.gz | 29.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zk/4zku ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zku | HTTPS FTP |
-Related structure data
Related structure data | 4zkpC 4zxqC 5bu5C 5bu8C 5bvzC 2pohS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 25075.744 Da / Num. of mol.: 2 / Mutation: L222M Source method: isolated from a genetically manipulated source Details: Bacteriophage P22 / Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 26 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P35837 #2: Chemical | #3: Chemical | #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: 2.95 Å3/Da / Density % sol: 58.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10 / Details: 40% PEG 4000, 0.1M CAPS pH 10.0 / PH range: 10 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2008 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. obs: 19166 / % possible obs: 96.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.083 / Net I/σ(I): 13.66 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.4 / % possible all: 84.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2POH Resolution: 2.5→28.82 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.18 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→28.82 Å
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Refine LS restraints |
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LS refinement shell |
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