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- PDB-7w1e: Crystal structure of Klebsiella pneumoniae K1 capsule-specific po... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7w1e | |||||||||
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Title | Crystal structure of Klebsiella pneumoniae K1 capsule-specific polysaccharide lyase in complex with products | |||||||||
![]() | K1 LYASE | |||||||||
![]() | VIRAL PROTEIN / BETA-HELIX / POLYSACCHARIDE LYASE / TAIL SPIKE PROTEIN / LYASE | |||||||||
Function / homology | ![]() symbiont entry into host cell via disruption of host cell glycocalyx / Lyases / symbiont entry into host cell via disruption of host cell envelope / virus tail / adhesion receptor-mediated virion attachment to host cell / lyase activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Tu, I.F. / Huang, K.F. / Wu, S.H. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use. Authors: Tu, I.F. / Lin, T.L. / Yang, F.L. / Lee, I.M. / Tu, W.L. / Liao, J.H. / Ko, T.P. / Wu, W.J. / Jan, J.T. / Ho, M.R. / Chou, C.Y. / Wang, A.H. / Wu, C.Y. / Wang, J.T. / Huang, K.F. / Wu, S.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11.4 MB | Display | ![]() |
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Full document | ![]() | 11.5 MB | Display | |
Data in XML | ![]() | 177.1 KB | Display | |
Data in CIF | ![]() | 273.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w1cC ![]() 7w1dC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 16 molecules ABCDEF
#1: Protein | Mass: 72130.633 Da / Num. of mol.: 6 / Mutation: D391A, D392A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: PET28A / Production host: ![]() ![]() #2: Polysaccharide | 3-O-acetyl-6-deoxy-alpha-L-galactopyranose-(1-3)-beta-D-glucopyranose Type: oligosaccharide / Mass: 368.334 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source |
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-Non-polymers , 4 types, 4919 molecules ![](data/chem/img/IMD.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/98X.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/98X.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-IMD / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-98X / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 15% (W/V) PEG 4000, 0.2 M IMIDAZOLE MALATE, PH 6.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2013 |
Radiation | Monochromator: LN2-COOLED, FIXED-EXIT DOUBLE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→30 Å / Num. obs: 673887 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 19.84 |
Reflection shell | Resolution: 1.46→1.51 Å / Redundancy: 2 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 2.14 / Num. unique obs: 66287 / % possible all: 92.9 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 108.77 Å2 / Biso mean: 18 Å2 / Biso min: 6.96 Å2
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Refinement step | Cycle: final / Resolution: 1.46→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.46→1.5 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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