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Open data
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Basic information
Entry | Database: PDB / ID: 7w16 | ||||||
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Title | Complex structure of alginate lyase AlyV with M8 | ||||||
![]() | alginate lyase | ||||||
![]() | LYASE / PL7 family / alginate lyase / complex | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, W.Z. / Lyu, Q.Q. / Li, Z.J. / Zhang, K.K. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements. Authors: Zhang, K. / Li, Z. / Zhu, Q. / Cao, H. / He, X. / Zhang, X.H. / Liu, W. / Lyu, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 120.9 KB | Display | ![]() |
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PDB format | ![]() | 95.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 817.9 KB | Display | ![]() |
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Full document | ![]() | 819.8 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: Protein | Mass: 33442.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Polysaccharide | beta-D-mannopyranuronic acid-(1-4)-beta-D-mannopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 65.87 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Sodium citrate tribasic dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 34336 / % possible obs: 100 % / Redundancy: 17.8 % / Rpim(I) all: 0.049 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 15.6 % / Mean I/σ(I) obs: 3.7 / Num. unique obs: 3385 / Rpim(I) all: 0.281 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.85 Å2 / Biso mean: 22.158 Å2 / Biso min: 4.02 Å2
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Refinement step | Cycle: final / Resolution: 1.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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