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Yorodumi- PDB-6wnu: Crystal structure of the three-domain cyclomaltodextrin glucanotr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wnu | ||||||||||||
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Title | Crystal structure of the three-domain cyclomaltodextrin glucanotransferase CldA in the monomeric form | ||||||||||||
Components | Cyclomaltodextrin glucanotransferase | ||||||||||||
Keywords | TRANSFERASE / Cyclodextrin / Extremozyme / GH13 family / Starch | ||||||||||||
Function / homology | Function and homology information alpha-amylase / alpha-amylase activity / carbohydrate metabolic process / calcium ion binding Similarity search - Function | ||||||||||||
Biological species | Caldanaerobacter subterraneus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.88 Å | ||||||||||||
Authors | Magana-Cuevas, E. / Centeno-Leija, S. / Serrano-Posada, H. | ||||||||||||
Funding support | Mexico, 3items
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Citation | Journal: To Be Published Title: Discovery of a novel group of three-domain thermophilic cyclomaltodextrin glucanotransferases: structural and functional implications. Authors: Centeno-Leija, S. / Lopez-Munguia, A. / Cardenas-Conejo, Y. / Mancilla-Margalli, N.A. / Velazquez-Cruz, B. / Magana-Cuevas, E. / Guerra-Borrego, Y. / Zatarain-Palacios, R. / Marin-Tovar, Y. ...Authors: Centeno-Leija, S. / Lopez-Munguia, A. / Cardenas-Conejo, Y. / Mancilla-Margalli, N.A. / Velazquez-Cruz, B. / Magana-Cuevas, E. / Guerra-Borrego, Y. / Zatarain-Palacios, R. / Marin-Tovar, Y. / Gomez-Manzo, S. / Marcial-Quino, J. / Hernandez-Ochoa, B. / Osuna-Castro, J.A. / Rudino-Pinera, E. / Serrano-Posada, H. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6wnu.cif.gz | 129.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wnu.ent.gz | 95.3 KB | Display | PDB format |
PDBx/mmJSON format | 6wnu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/6wnu ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wnu | HTTPS FTP |
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-Related structure data
Related structure data | 6wniC 1qhoS 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: 61203.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caldanaerobacter subterraneus (bacteria) Gene: O163_00610 / Plasmid: PET-22B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS References: UniProt: U5CJP3, cyclomaltodextrin glucanotransferase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-PEG / #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: 2.38 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 291 K / Method: microbatch / pH: 5.5 Details: 0.1 M ammonium acetate, 0.1 M Bis-Tris pH 5.5, 17%(w/v) PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.19499 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 8, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.19499 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→30.1 Å / Num. obs: 43950 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 25.9 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 1.88→1.92 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.797 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2853 / CC1/2: 0.917 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1QHO Resolution: 1.88→30.08 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 26.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.52 Å2 / Biso mean: 28.5288 Å2 / Biso min: 11.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.88→30.08 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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