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Yorodumi- PDB-6iyg: The Structure of Maltooligosaccharide-forming Amylase from Pseudo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6iyg | |||||||||
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Title | The Structure of Maltooligosaccharide-forming Amylase from Pseudomonas saccharophila STB07 with Maltotetraose | |||||||||
Components | Glucan 1,4-alpha-maltotetraohydrolase | |||||||||
Keywords | SUGAR BINDING PROTEIN / Maltooligosaccharide-forming Amylase / Pseudomonas saccharophila STB07 | |||||||||
Function / homology | Function and homology information glucan 1,4-alpha-maltotetraohydrolase / glucan 1,4-alpha-maltotetraohydrolase activity / starch catabolic process / starch binding / alpha-amylase activity / extracellular space / metal ion binding Similarity search - Function | |||||||||
Biological species | Pelomonas saccharophila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | |||||||||
Authors | Li, Z.F. / Ban, X.F. / Zhang, Z.Q. / Li, C.M. / Gu, Z.B. / Jin, T.C. / Li, Y.L. / Shang, Y.H. | |||||||||
Funding support | China, 2items
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Citation | Journal: To Be Published Title: Maltotetraose-forming amylase from Pseudomonas saccharophila STB07 Authors: Zhang, Z.Q. / Ban, X.F. / Li, Z.F. / Jin, T.C. / Li, Y.L. / Gu, Z.B. / Li, C.M. / Shang, Y.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iyg.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iyg.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 6iyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6iyg_validation.pdf.gz | 793.7 KB | Display | wwPDB validaton report |
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Full document | 6iyg_full_validation.pdf.gz | 795.1 KB | Display | |
Data in XML | 6iyg_validation.xml.gz | 20.3 KB | Display | |
Data in CIF | 6iyg_validation.cif.gz | 30.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iyg ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iyg | HTTPS FTP |
-Related structure data
Related structure data | 6j3xC 6iwkS 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
#1: Protein | Mass: 58622.742 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pelomonas saccharophila (bacteria) / Gene: mta / Production host: Bacillus subtilis (bacteria) References: UniProt: P22963, glucan 1,4-alpha-maltotetraohydrolase | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose | ||||
#3: Chemical | ChemComp-EDO / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.86 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M ammonium sulfate, 0.02 M Tris-HCl, 0.02 M maltotetraose |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97891 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→42.436 Å / Num. obs: 80886 / % possible obs: 98.61 % / Redundancy: 6 % / CC1/2: 0.843 / Net I/σ(I): 2 |
Reflection shell | Resolution: 1.5→1.5177 Å / Num. unique obs: 1124 / CC1/2: 0.815 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6IWK Resolution: 1.5→42.436 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 88.44 Å2 / Biso mean: 29.8288 Å2 / Biso min: 16.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→42.436 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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