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- PDB-5gmt: Crystal structure of the marine PL-14 alginate lyase from Aplysia... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5gmt | ||||||
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Title | Crystal structure of the marine PL-14 alginate lyase from Aplysia kurodai | ||||||
![]() | Alginate lyase | ||||||
![]() | LYASE / alginate lyase / polysaccharide lyase family 14 / glycosidic bond / beta-D-mannuronic acid / alpha-L-guluronic acid | ||||||
Function / homology | lyase activity / Alginate lyase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, H.-M. / Miyakawa, T. / Nakamura, A. / Tanokura, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14. Authors: Qin, H.M. / Miyakawa, T. / Inoue, A. / Nishiyama, R. / Nakamura, A. / Asano, A. / Sawano, Y. / 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 | ![]() | 119.7 KB | Display | ![]() |
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PDB format | ![]() | 96.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.6 KB | Display | ![]() |
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Full document | ![]() | 423.9 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 35 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31169.584 Da / Num. of mol.: 2 / Fragment: UNP residues 29-295 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: E7FLQ2, mannuronate-specific alginate lyase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, PEG3350, Ammonium acetate |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 13, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→50 Å / Num. obs: 42279 / % possible obs: 94.8 % / Redundancy: 2 % / Rsym value: 0.034 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.77→1.82 Å / Rsym value: 0.141 |
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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: 1.77→36.173 Å
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Refine LS restraints |
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LS refinement shell |
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