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- PDB-3gd9: Crystal structure of laminaripentaose-producing beta-1,3-glucanas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gd9 | |||||||||
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Title | Crystal structure of laminaripentaose-producing beta-1,3-glucanase in complex with laminaritetraose | |||||||||
![]() | Laminaripentaose-producing beta-1,3-guluase (LPHase) | |||||||||
![]() | HYDROLASE / Glycoside hydrolases / Laminaripentaose-producing beta-1 / 3-glucnase (LPHase) / Multi-wavelength anomalous dispersion (MAD) | |||||||||
Function / homology | ![]() Beta-1,3-glucanase, C-terminal domain / Beta-1,3-glucanase, N-terminal, subdomain 2 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Metal Transport, Frataxin; Chain A / Thaumatin / Thaumatin / Osmotin/thaumatin-like superfamily ...Beta-1,3-glucanase, C-terminal domain / Beta-1,3-glucanase, N-terminal, subdomain 2 / Glycosyl hydrolases family 64 (GH64) domain profile. / Beta-1,3-glucanase, N-terminal / Glucan endo-1,3-beta-glucosidase / Beta-1,3-glucanase / Metal Transport, Frataxin; Chain A / Thaumatin / Thaumatin / Osmotin/thaumatin-like superfamily / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wu, H.M. / Hsu, M.T. / Liu, S.W. / Lai, C.C. / Li, Y.K. / Wang, W.C. | |||||||||
![]() | ![]() Title: Structure, mechanistic action, and essential residues of a GH-64 enzyme, laminaripentaose-producing beta-1,3-glucanase. Authors: Wu, H.M. / Liu, S.W. / Hsu, M.T. / Hung, C.L. / Lai, C.C. / Cheng, W.C. / Wang, H.J. / Li, Y.K. / Wang, W.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.2 KB | Display | ![]() |
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PDB format | ![]() | 73.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 758.5 KB | Display | ![]() |
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Full document | ![]() | 764.7 KB | Display | |
Data in XML | ![]() | 23.2 KB | Display | |
Data in CIF | ![]() | 36.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3gd0SC 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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Unit cell |
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Components
#1: Protein | Mass: 39592.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Z4I2, glucan endo-1,3-beta-D-glucosidase |
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#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.93 % |
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Crystal grow | Temperature: 293 K / Method: liquid diffusion / pH: 6.5 Details: 0.05M ammonium sulfate, 20% PEG8000, 0.1M sodium cacodylate (pH6.5), 20mM laminaripentaose, LIQUID DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2006 |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 39457 / Num. obs: 38270 / % possible obs: 97 % / Observed criterion σ(F): 325.5 / Observed criterion σ(I): 103.9 / Redundancy: 8.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.038 / Net I/σ(I): 41.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.117 / Mean I/σ(I) obs: 19.5 / Num. unique all: 3462 / Rsym value: 0.104 / % possible all: 89.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3GD0 Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.171 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 18.709 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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