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- PDB-6wni: Crystal structure of CldA, the first cyclomaltodextrin glucanotra... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6wni | ||||||||||||
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Title | Crystal structure of CldA, the first cyclomaltodextrin glucanotransferase with a three-domain ABC distribution | ||||||||||||
![]() | Cyclomaltodextrin glucanotransferase![]() | ||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() ![]() | ||||||||||||
![]() | Magana-Cuevas, E. / Centeno-Leija, S. / Serrano-Posada, H. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 241.1 KB | Display | ![]() |
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PDB format | ![]() | 188.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6wnuC ![]() 1qhoS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 61203.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: O163_00610 / Plasmid: PET-22B / Production host: ![]() ![]() ![]() References: UniProt: U5CJP3, ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-FLC / ![]() #4: Chemical | ChemComp-PEG / ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46 % |
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Crystal grow![]() | Temperature: 291 K / Method: microbatch / pH: 5.1 / Details: 0.2 M ammonium citrate dibasic, 20%(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
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![]() |
Reflection | Resolution: 1.66→28.54 Å / Num. obs: 121677 / % possible obs: 99.5 % / Redundancy: 7.4 % / Biso Wilson estimate: 20.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.3 |
Reflection shell | Resolution: 1.66→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2 / Num. unique obs: 5577 / CC1/2: 0.674 / % possible all: 92.8 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1QHO Resolution: 1.66→28.502 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.5
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 75.81 Å2 / Biso mean: 24.2611 Å2 / Biso min: 10.21 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→28.502 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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