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- PDB-3d5z: 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: 3d5z | |||||||||
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Title | Crystal Structure Analysis of 1,5-alpha-arabinanase catalytic mutant (AbnBE201A) complexed to arabinotriose | |||||||||
![]() | 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 | ![]() | 81.4 KB | Display | ![]() |
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PDB format | ![]() | 58.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 709.8 KB | Display | ![]() |
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Full document | ![]() | 714.5 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 22.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3cu9SC ![]() 3d5yC ![]() 3d60C ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 35545.527 Da / Num. of mol.: 1 / Mutation: E201A 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: Polysaccharide | alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-beta-L-arabinofuranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Sequence details | THE 9TH RESIDUE, GLY, IS NOT A PLANNED MUTATION BUT A MUTATION IN THE CURRENT MODELS. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop, cocrystaliization / pH: 7.5 Details: 1.8M lithium sulfate, 0.1M Tris buffer 7.5, 5% (w/v) PEG 400, 3mM arabinotriose, Vapor diffusion, Hanging drop, Cocrystaliization, 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: Aug 10, 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→50 Å / Num. all: 22884 / Num. obs: 19994 / Observed criterion σ(F): 1 / Redundancy: 4.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.058 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.396 / Num. unique all: 894 / Rsym value: 0.429 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CU9 Resolution: 1.9→28.71 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 548343.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.5725 Å2 / ksol: 0.385006 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→28.71 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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