+Open data
-Basic information
Entry | Database: PDB / ID: 1ijg | ||||||
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Title | Structure of the Bacteriophage phi29 Head-Tail Connector Protein | ||||||
Components | UPPER COLLAR PROTEIN | ||||||
Keywords | VIRAL PROTEIN / alpha-helical bundle / RNA binding motif | ||||||
Function / homology | Function and homology information viral portal complex / viral procapsid / symbiont genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / RNA binding Similarity search - Function | ||||||
Biological species | Bacillus phage phi29 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Simpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Structure determination of the head-tail connector of bacteriophage phi29. Authors: Simpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M.O. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ijg.cif.gz | 628.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ijg.ent.gz | 523.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ijg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ijg_validation.pdf.gz | 554.5 KB | Display | wwPDB validaton report |
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Full document | 1ijg_full_validation.pdf.gz | 685.4 KB | Display | |
Data in XML | 1ijg_validation.xml.gz | 126 KB | Display | |
Data in CIF | 1ijg_validation.cif.gz | 170.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ijg ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ijg | HTTPS FTP |
-Related structure data
Related structure data | 1jnbC 1fouS 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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1 |
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Unit cell |
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Details | The biological assembly is a dodecamer luckily comprising the asymmetric unit. |
-Components
#1: Protein | Mass: 35917.293 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage phi29 (virus) / Genus: Phi29-like viruses / Gene: 10 / Production host: Escherichia coli (E. coli) / References: UniProt: P04332 #2: 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: 3.56 Å3/Da / Density % sol: 65.21 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: MPD, calcium cloride, tris buffer, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 15, 1999 / Details: bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: bend cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. all: 112772 / Num. obs: 110311 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 58.4 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 28.9 |
Reflection shell | Resolution: 2.9→2.92 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.333 / % possible all: 99.6 |
Reflection | *PLUS Redundancy: 3.54 % |
Reflection shell | *PLUS % possible obs: 99 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FOU Resolution: 2.9→500 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 54.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.363 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→500 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.92 Å / Total num. of bins used: 50
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.9 Å / Lowest resolution: 500 Å / σ(F): 0 / % reflection Rfree: 2.27 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 54.2 Å2 | |||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.29 / % reflection Rfree: 2.5 % / Rfactor Rwork: 0.324 |