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- PDB-5y33: Crystal structure of alginate lyase from Flavobacterium sp. UMI-0... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5y33 | ||||||
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Title | Crystal structure of alginate lyase from Flavobacterium sp. UMI-01 reveals polymannuronate specificity | ||||||
![]() | Alginate lyase | ||||||
![]() | STRUCTURAL PROTEIN / alginate lyase / b-elimination reaction / b-jelly roll fold / endolytic enzyme | ||||||
Function / homology | Alginate lyase 2 / Alginate lyase / hydrolase activity, hydrolyzing O-glycosyl compounds / Concanavalin A-like lectin/glucanase domain superfamily / carbohydrate metabolic process / lyase activity / Alginate lyase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, H.-M. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | ||||||
![]() | ![]() Title: Structural basis for controlling the enzymatic properties of polymannuronate preferred alginate lyase FlAlyA from the PL-7 family. Authors: Qin, H.M. / Miyakawa, T. / Inoue, A. / Nishiyama, R. / Nakamura, A. / Asano, A. / Ojima, T. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 416.5 KB | Display | ![]() |
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Full document | ![]() | 416.8 KB | Display | |
Data in XML | ![]() | 14.8 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 29901.758 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 29-288 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M DL-malic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 12, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 43349 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.039 / Net I/σ(I): 38.5 |
Reflection shell | Resolution: 1.54→1.58 Å / Rsym value: 1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.54→31.069 Å
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Refine LS restraints |
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LS refinement shell |
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