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- PDB-7cn7: T4 phage spackle protein gp61.3 complex with lysozyme domain of g... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cn7 | |||||||||
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Title | T4 phage spackle protein gp61.3 complex with lysozyme domain of gp5 tail lysozyme | |||||||||
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![]() | VIRAL PROTEIN / Lysozyme inhibitor complex / Phage / Lysis inhibition | |||||||||
Function / homology | ![]() superinfection exclusion / host cell periplasmic space / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process ...superinfection exclusion / host cell periplasmic space / symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kanamaru, S. / Leiman, P.G. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Function of the T4 Spackle Protein Gp61.3. Authors: Kanamaru, S. / Uchida, K. / Nemoto, M. / Fraser, A. / Arisaka, F. / Leiman, P.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 | ![]() | 230.4 KB | Display | ![]() |
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PDB format | ![]() | 153.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 707.2 KB | Display | ![]() |
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Full document | ![]() | 709.3 KB | Display | |
Data in XML | ![]() | 16.4 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7cn6C ![]() 1k28S 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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Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 20353.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. / Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 8688.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 5 types, 384 molecules ![](data/chem/img/1PG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-1PG / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.26 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.4 / Details: PEG550MME, MES, KSCN |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 3, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→46.72 Å / Num. obs: 187608 / % possible obs: 99.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 10.29 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 1.01 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 1.15→1.17 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 0.859 / Num. unique obs: 4655 / CC1/2: 0.859 / Rpim(I) all: 0.23 / Rrim(I) all: 0.59 / Χ2: 1.01 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1k28 Resolution: 1.15→17.92 Å / SU ML: 0.0849 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 10.4462 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 16.28 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→17.92 Å
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Refine LS restraints |
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LS refinement shell |
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