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- PDB-4ku0: Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ku0 | ||||||
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Title | Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-helix fragment | ||||||
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![]() | HYDROLASE/PROTEIN BINDING / PAAR-repeat motif / membrane piercing / type VI secretion system / T6SS / cell puncturing device / beta-helix / gp5-gp27 protein complex / HYDROLASE-PROTEIN BINDING complex | ||||||
Function / homology | ![]() peptidoglycan beta-N-acetylmuramidase activity / 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 ...peptidoglycan beta-N-acetylmuramidase activity / 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 / metal ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Buth, S.A. / Leiman, P.G. / Shneider, M.M. | ||||||
![]() | ![]() Title: Crystall structute of the business end of the T4 cell-puncturing device Authors: Buth, S.A. / Leiman, P.G. / Shneider, M.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 148.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 840.9 KB | Display | ![]() |
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Full document | ![]() | 847.6 KB | Display | |
Data in XML | ![]() | 28.8 KB | Display | |
Data in CIF | ![]() | 39.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4jj2S S: Starting model for refinement |
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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, 4 molecules ABCD
#1: Protein | Mass: 9856.678 Da / Num. of mol.: 3 / Fragment: residues 484-575 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 10102.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 571 molecules 














#3: Chemical | ChemComp-MG / | ||||||||||
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#4: Chemical | ChemComp-ELA / | ||||||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-STE / | #7: Chemical | ChemComp-PLM / | #8: Chemical | ChemComp-FE / | #9: Chemical | ChemComp-NA / | #10: Water | ChemComp-HOH / | |
-Details
Has protein modification | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.87 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 23-25% PEG 3350, 100mM Tris pH=8.5, 40-100mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2012 / Details: dynamically bendable mirror |
Radiation | Monochromator: Si(111) monochromator / 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 Å / Num. all: 129006 / Num. obs: 124490 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.13 % / Biso Wilson estimate: 18.103 Å2 / Rmerge(I) obs: 0.0532 / Net I/σ(I): 12.12 |
Reflection shell | Resolution: 1.15→1.22 Å / Redundancy: 4.12 % / Mean I/σ(I) obs: 2.27 / Num. unique all: 21326 / % possible all: 81.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4JJ2 Resolution: 1.15→46 Å / Num. parameters: 31827 / Num. restraintsaints: 40407 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
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Refine analyze | Num. disordered residues: 23 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3356.94 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→46 Å
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Refine LS restraints |
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