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Yorodumi- PDB-6jfj: Crystal structure of Pullulanase from Paenibacillus barengoltzii ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jfj | ||||||||||||
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Title | Crystal structure of Pullulanase from Paenibacillus barengoltzii complex with maltohexaose and alpha-cyclodextrin | ||||||||||||
Components | Pulullanase | ||||||||||||
Keywords | HYDROLASE / GH13 / Pullulanase / alpha-cyclodextrin / Maltohexaose | ||||||||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Paenibacillus barengoltzii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.932 Å | ||||||||||||
Authors | Wu, S.W. / Yang, S.Q. / Qin, Z. / You, X. / Huang, P. / Jiang, Z.Q. | ||||||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jfj.cif.gz | 164.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jfj.ent.gz | 123.9 KB | Display | PDB format |
PDBx/mmJSON format | 6jfj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jfj_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6jfj_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6jfj_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 6jfj_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/6jfj ftp://data.pdbj.org/pub/pdb/validation_reports/jf/6jfj | HTTPS FTP |
-Related structure data
Related structure data | 6jeqC 6jfxC 6jhfC 2e8yS C: citing same article (ref.) S: Starting model for refinement |
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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 , 1 types, 1 molecules A
#1: Protein | Mass: 75183.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues 1-8 (MLSVQKEF) and 638-658 (GASGEAAAAAPAAAGGPPAGG) had low-level electron density and were not included in the model. Source: (gene. exp.) Paenibacillus barengoltzii (bacteria) / Strain: CAU904 / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C5GWS2, pullulanase |
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-Sugars , 2 types, 3 molecules
#2: Polysaccharide | #3: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose | |
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-Non-polymers , 9 types, 473 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-PEG / #6: Chemical | #7: Chemical | ChemComp-1PE / | #8: Chemical | #9: Chemical | ChemComp-IMD / #10: Chemical | #11: Chemical | ChemComp-CL / #12: 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: 2.28 Å3/Da / Density % sol: 46.15 % |
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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: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97776 Å |
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: 1.932→50 Å / Num. obs: 52278 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 1.932→1.96 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.6 / Num. unique obs: 2657 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2E8Y Resolution: 1.932→49.09 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.43 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: 1.932→49.09 Å
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Refine LS restraints |
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LS refinement shell |
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