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- PDB-3d60: Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mut... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3d60 | ||||||
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Title | Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (D27A) | ||||||
![]() | Intracellular arabinanase | ||||||
![]() | HYDROLASE / Arabinanase / Glycosyl Hydrolase / beta-propeller / Geobacillus stearothermophilus | ||||||
Function / homology | ![]() arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Alhassid, A. / Ben David, A. / Shoham, Y. / Shoham, G. | ||||||
![]() | ![]() Title: Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate Authors: Alhassid, A. / Ben-David, A. / Tabachnikov, O. / Libster, D. / Naveh, E. / Zolotnitsky, G. / Shoham, Y. / Shoham, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.4 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.3 KB | Display | ![]() |
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Full document | ![]() | 429.4 KB | Display | |
Data in XML | ![]() | 15.5 KB | Display | |
Data in CIF | ![]() | 22 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cu9SC ![]() 3d5yC ![]() 3d5zC ![]() 3d61C 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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Components
#1: Protein | Mass: 35616.605 Da / Num. of mol.: 1 / Mutation: D27A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: T-6 / Gene: abn / Plasmid: pET9d / Production host: ![]() ![]() References: UniProt: B3EYM8, arabinan endo-1,5-alpha-L-arabinanase |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.75M lithium sulfate, 0.1M Tris buffer pH 8.5, 3% (w/v) PGME 2000, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 19, 2006 |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 24489 / Num. obs: 23506 / % possible obs: 96 % / Observed criterion σ(F): 1 / Redundancy: 7.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.055 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.9→1.94 Å / Rmerge(I) obs: 0.36 / Num. unique all: 1121 / Rsym value: 0.406 / % possible all: 93.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CU9 Resolution: 1.9→28.92 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 480062.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.5155 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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