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Open data
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Basic information
Entry | Database: PDB / ID: 1ijg | ||||||
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Title | Structure of the Bacteriophage phi29 Head-Tail Connector Protein | ||||||
![]() | UPPER COLLAR PROTEIN | ||||||
![]() | VIRAL PROTEIN / alpha-helical bundle / RNA binding motif | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Simpson, A.A. / Leiman, P.G. / Tao, Y. / He, Y. / Badasso, M. / Jardine, P.J. / Anderson, D.L. / Rossmann, M.G. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 628.7 KB | Display | ![]() |
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PDB format | ![]() | 523.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 554.5 KB | Display | ![]() |
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Full document | ![]() | 685.4 KB | Display | |
Data in XML | ![]() | 126 KB | Display | |
Data in CIF | ![]() | 170.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1jnbC ![]() 1fouS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a dodecamer luckily comprising the asymmetric unit. |
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Components
#1: Protein | Mass: 35917.293 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 % |
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Processing
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Refinement | Method to determine structure: ![]() 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 |