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- PDB-6jfx: Crystal structure of Pullulanase from Paenibacillus barengoltzii ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6jfx | ||||||||||||
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Title | Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with maltopentaose | ||||||||||||
![]() | Pulullanase | ||||||||||||
![]() | HYDROLASE / GH13 / Pullulanase / maltopentaose | ||||||||||||
Function / homology | ![]() pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | ||||||||||||
![]() | ![]() Title: Structural basis of carbohydrate binding in domain C of a type I pullulanase from Paenibacillus barengoltzii. Authors: Huang, P. / Wu, S. / Yang, S. / Yan, Q. / Jiang, Z. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.3 KB | Display | ![]() |
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PDB format | ![]() | 120.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 43.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jeqC ![]() 6jfjC ![]() 6jhfC ![]() 2e8yS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 4 molecules A
#1: Protein | Mass: 75183.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-8 and 641-657 had low-level electron density and were not included in the model. Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: A0A0C5GWS2, pullulanase |
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#2: Polysaccharide |
-Non-polymers , 8 types, 465 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/IMD.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PGE / | #6: Chemical | #7: Chemical | ChemComp-IMD / | #8: Chemical | ChemComp-CA / | #9: Chemical | ChemComp-CL / #10: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.08M calcium chloride, 0.1M MES, 22% PEG 3350, 0.7% beta-OG, pH 6.5 Temp details: 291.0-295.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: 90-100 / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97776 Å / Relative weight: 1 |
Reflection | Resolution: 1.981→50 Å / Num. obs: 49297 / % possible obs: 99.8 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 19.833 |
Reflection shell | Resolution: 1.981→2.052 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 4616 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2E8Y Resolution: 1.981→47.213 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.83 Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.981→47.213 Å
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Refine LS restraints |
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LS refinement shell |
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