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- PDB-2x6y: Tailspike protein mutant D339A of E.coli bacteriophage HK620 in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2x6y | |||||||||
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Title | Tailspike protein mutant D339A of E.coli bacteriophage HK620 in complex with hexasaccharide | |||||||||
![]() | TAIL SPIKE PROTEIN | |||||||||
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Function / homology | ![]() biological process involved in interaction with host / ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lorenzen, N.K. / Mueller, J.J. / Heinemann, U. / Seckler, R. / Barbirz, S. | |||||||||
![]() | ![]() Title: Single Amino Acid Exchange in Bacteriophage Hk620 Tailspike Protein Results in Thousand-Fold Increase of its Oligosaccharide Affinity. Authors: Broeker, N.K. / Gohlke, U. / Muller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S. #1: ![]() Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related. Authors: Barbirz, S. / Muller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 276.3 KB | Display | ![]() |
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PDB format | ![]() | 219.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2x6wC ![]() 2x6xC ![]() 2x85C ![]() 4avzC ![]() 2vjiS C: citing same article ( 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 64661.348 Da / Num. of mol.: 1 Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710 Mutation: YES Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH HEXASACCHARIDE / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||||
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#2: Polysaccharide | alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||||||
#3: Chemical | #4: Chemical | ChemComp-TRS / | ![]() #5: Water | ChemComp-HOH / | ![]() Compound details | ENGINEERED | Sequence details | DELETION 1-110, MUTATION D339A | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.48 % / Description: NONE |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL. RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO ...Details: VAPOR DIFFUSION, HANGING DROP:PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8,2MM EDTA,0.2M NACL. RERVOIR: 100MM TRIS PH8.5,3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICRO LITER, 0.3 MICRO LITER 33MM HEXASACCHARIDE. TEMPERATURE 20 DEGREE CELSIUS. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX / Detector: CCD / Date: Oct 2, 2009 / Details: GLAS MIRROR |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.35→37.17 Å / Num. obs: 112857 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.35→1.39 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 58.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2VJI Resolution: 1.35→43.22 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.923 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→43.22 Å
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Refine LS restraints |
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