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Yorodumi- PDB-3d5y: High resolution crystal structure of 1,5-alpha-arabinanase cataly... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d5y | ||||||
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Title | High resolution crystal structure of 1,5-alpha-arabinanase catalytic mutant (AbnBE201A) | ||||||
Components | Intracellular arabinanase | ||||||
Keywords | HYDROLASE / Arabinanase / Glycosyl Hydrolase / High resolution / beta-propeller / Geobacillus stearothermophilus | ||||||
Function / homology | Function and homology information 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 | Geobacillus stearothermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.22 Å | ||||||
Authors | Alhassid, A. / Ben David, A. / Shoham, Y. / Shoham, G. | ||||||
Citation | Journal: Biochem.J. / Year: 2009 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3d5y.cif.gz | 131.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d5y.ent.gz | 100.6 KB | Display | PDB format |
PDBx/mmJSON format | 3d5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/3d5y ftp://data.pdbj.org/pub/pdb/validation_reports/d5/3d5y | HTTPS FTP |
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-Related structure data
Related structure data | 3cu9SC 3d5zC 3d60C 3d61C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: 35545.527 Da / Num. of mol.: 1 / Mutation: E201A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: T-6 / Gene: abn / Plasmid: pET9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: B3EYM8, arabinan endo-1,5-alpha-L-arabinanase |
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#2: Chemical | ChemComp-CA / |
#3: 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.83 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 1.9M lithium sulfate, 0.1M Tris buffer pH 8.5, 4%(w/v) PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978578 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2005 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978578 Å / Relative weight: 1 |
Reflection | Resolution: 1.22→50 Å / Num. all: 86543 / Num. obs: 83088 / % possible obs: 96 % / Redundancy: 16 % / Biso Wilson estimate: 11.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.059 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.22→1.24 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.24 / Num. unique all: 3707 / Rsym value: 0.268 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: PDB ENTRY 3CU9 Resolution: 1.22→30 Å / Num. parameters: 21381 / Num. restraintsaints: 26021 / Isotropic thermal model: Anisotropic / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Displacement parameters | Biso mean: 17.8 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2797.5
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Refinement step | Cycle: LAST / Resolution: 1.22→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.22→1.3 Å / Rfactor Rfree error: 0.007
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