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- PDB-6sed: Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sed | ||||||
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Title | Cold-adapted beta-D-galactosidase from Arthrobacter sp. 32cB in complex with galactose | ||||||
![]() | Beta-galactosidase | ||||||
![]() | HYDROLASE / galactosidase / cold-adapted / psychrophilic / dimeric | ||||||
Function / homology | ![]() lactose catabolic process / beta-galactosidase complex / beta-galactosidase / beta-galactosidase activity / carbohydrate binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rutkiewicz, M. / Bujacz, A. / Kaminska, P. / Bujacz, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-d-galactosidase fromArthrobactersp. 32cB. Authors: Rutkiewicz, M. / Bujacz, A. / Wanarska, M. / Wierzbicka-Wos, A. / Cieslinski, H. #1: ![]() Title: Structural features of cold-adapted dimeric GH2 beta-D-galactosidase from Arthrobacter sp. 32cB. Authors: Rutkiewicz, M. / Bujacz, A. / Bujacz, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 425 KB | Display | ![]() |
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PDB format | ![]() | 343.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 845.8 KB | Display | ![]() |
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Full document | ![]() | 850 KB | Display | |
Data in XML | ![]() | 40.3 KB | Display | |
Data in CIF | ![]() | 60.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6se8C ![]() 6se9C ![]() 6seaC ![]() 6sebC ![]() 6secC ![]() 6etzS 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/GAL.gif)
![](data/chem/img/GAL.gif)
#1: Protein | Mass: 109764.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Sugar | ChemComp-GAL / |
-Non-polymers , 5 types, 621 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MLI.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ACT / #4: Chemical | ChemComp-MLI / | #5: Chemical | ChemComp-FMT / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.35 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 40% Tacsimate pH 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2017 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→46.516 Å / Num. obs: 80260 / % possible obs: 99.8 % / Redundancy: 10.076 % / Biso Wilson estimate: 37.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.136 / Χ2: 1.216 / Net I/σ(I): 16.07 / Num. measured all: 808666 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6ETZ Resolution: 2.233→46.516 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.27
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 197.4 Å2 / Biso mean: 48.1031 Å2 / Biso min: 26.98 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.233→46.516 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 41.4379 Å / Origin y: 27.1459 Å / Origin z: 17.6278 Å
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Refinement TLS group |
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