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Open data
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Basic information
Entry | Database: PDB / ID: 7w13 | ||||||
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Title | Complex structure of alginate lyase PyAly with M8 | ||||||
![]() | Alginate lyase | ||||||
![]() | LYASE / PL7 family / alginate lyase / complex | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / Concanavalin A-like lectin/glucanase domain superfamily / lyase activity / Alginate lyase![]() | ||||||
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 | ![]() | 58.9 KB | Display | ![]() |
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PDB format | ![]() | 40.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 727.7 KB | Display | ![]() |
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Full document | ![]() | 729.2 KB | Display | |
Data in XML | ![]() | 10.9 KB | Display | |
Data in CIF | ![]() | 14.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7w12C ![]() 7w16C ![]() 7w18C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 27055.221 Da / Num. of mol.: 1 / Mutation: H125A 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-(1-4)-beta-D-mannopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.87 % |
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Crystal grow | Temperature: 288.15 K / Method: vapor diffusion, hanging drop / Details: Imidazole, Jeffamine ED-2001 |
-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: May 24, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→50 Å / Num. obs: 29611 / % possible obs: 99.9 % / Redundancy: 12.8 % / Rsym value: 0.077 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.62→1.65 Å / Num. unique obs: 1467 / Rsym value: 0.077 / % possible all: 100 |
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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: 54.09 Å2 / Biso mean: 14.153 Å2 / Biso min: 6.66 Å2
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Refinement step | Cycle: final / Resolution: 1.65→39.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.693 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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