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- PDB-1r8l: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis -
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Open data
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Basic information
Entry | Database: PDB / ID: 1r8l | ||||||
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Title | The structure of endo-beta-1,4-galactanase from Bacillus licheniformis | ||||||
![]() | endo-beta-1,4-galactanase | ||||||
![]() | HYDROLASE / (beta-alpha)8-barrel / calcium ion / glycosyl hydrolase / family 53 / clan GH-A | ||||||
Function / homology | ![]() arabinogalactan endo-beta-1,4-galactanase / arabinogalactan endo-1,4-beta-galactosidase activity / glucosidase activity / pectin catabolic process / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ryttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L. / Bjornvad, M. / Larsen, S. | ||||||
![]() | ![]() Title: The structure of endo-beta-1,4-galactanase from Bacillus licheniformis in complex with two oligosaccharide products Authors: Ryttersgaard, C. / Le Nours, J. / Lo Leggio, L. / Jorgensen, C.T. / Christensen, L.L. / Bjornvad, M. / Larsen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 159 KB | Display | ![]() |
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PDB format | ![]() | 125.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.1 KB | Display | ![]() |
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Full document | ![]() | 447.6 KB | Display | |
Data in XML | ![]() | 29.3 KB | Display | |
Data in CIF | ![]() | 40.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ur0C ![]() 1ur4C ![]() 1fhlS 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | The biological assembly is a monomer of either chain A or B |
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Components
#1: Protein | Mass: 43778.434 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q65CX5, arabinogalactan endo-beta-1,4-galactanase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: PEG 1500, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Sep 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→19.67 Å / Num. all: 25224 / Num. obs: 25224 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 38.871 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.61 |
Reflection shell | Resolution: 2.6→2.64 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / Num. unique all: 1239 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDN ENTRY 1FHL Resolution: 2.6→19.67 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 31.7 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016
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