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Yorodumi- PDB-5yna: Crystal structure of Pullulanase from Klebsiella pneumoniae compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yna | |||||||||
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Title | Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 1 mM alpha-cyclodextrin | |||||||||
Components | PulA protein | |||||||||
Keywords | HYDROLASE / alpha-amylase / pullulanase / Klebsiella pneumoniae / crystal / co-crystallization / alpha-cyclodextrin | |||||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | |||||||||
Authors | Saka, N. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B. | |||||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin Authors: Saka, N. / Iwamoto, H. / Malle, D. / Takahashi, N. / Mizutani, K. / Mikami, B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yna.cif.gz | 235.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yna.ent.gz | 180.4 KB | Display | PDB format |
PDBx/mmJSON format | 5yna.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/5yna ftp://data.pdbj.org/pub/pdb/validation_reports/yn/5yna | HTTPS FTP |
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-Related structure data
Related structure data | 5yn2C 5yn7C 5yncC 5yndC 5yneC 5ynhC 2fgzS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 119318.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Klebsiella pneumoniae (bacteria) / References: UniProt: W9BQ28 |
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#2: Polysaccharide | Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin / Α-Cyclodextrin |
-Non-polymers , 5 types, 506 molecules
#3: Chemical | ChemComp-CA / #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M magnesium sulfate, 20%(w/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→50 Å / Num. obs: 87863 / % possible obs: 99.87 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.07552 / Net I/σ(I): 22.35 |
Reflection shell | Resolution: 1.96→2.03 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.4745 / Mean I/σ(I) obs: 4.34 / Num. unique obs: 8666 / CC1/2: 0.93 / % possible all: 99.94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FGZ Resolution: 1.96→44.151 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.96→44.151 Å
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Refine LS restraints |
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LS refinement shell |
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