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- PDB-3azy: Crystal structure of the laminarinase catalytic domain from Therm... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3azy | ||||||
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Title | Crystal structure of the laminarinase catalytic domain from Thermotoga maritima MSB8 | ||||||
![]() | Laminarinase | ||||||
![]() | HYDROLASE / beta-jelly roll fold / Glycosyl hydrolase family 16 / Laminarinase / Endo-1 / 3-beta-glucanase | ||||||
Function / homology | ![]() hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Jeng, W.Y. / Wang, N.C. / Wang, A.H.J. | ||||||
![]() | ![]() Title: Crystal structures of the laminarinase catalytic domain from Thermotoga maritima MSB8 in complex with inhibitors: essential residues for beta-1,3 and beta-1,4 glucan selection. Authors: Jeng, W.Y. / Wang, N.C. / Lin, C.T. / Shyur, L.F. / Wang, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 443.5 KB | Display | ![]() |
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PDB format | ![]() | 364.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3azxSC ![]() 3azzC ![]() 3b00C ![]() 3b01C 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: 31236.436 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 204-466 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9WXN1, glucan endo-1,3-beta-D-glucosidase #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.11 Å3/Da / Density % sol: 60.45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 41-46% (w/v) polypropylenglycol P400, 0.05-0.2M (NH4)2SO4, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 24, 2010 Details: Vertically Collimating Premirror, Toroidal Focusing Mirror |
Radiation | Monochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→30 Å / Num. all: 183497 / Num. obs: 183216 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 33.4 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 3.2 / Num. unique all: 18166 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3AZX Resolution: 1.65→24.6 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.929 / SU ML: 0.046 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.074 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.738 Å / Total num. of bins used: 10
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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