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Yorodumi- PDB-1jib: Complex of Alpha-amylase II (TVA II) from Thermoactinomyces vulga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jib | |||||||||
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Title | Complex of Alpha-amylase II (TVA II) from Thermoactinomyces vulgaris R-47 with Maltotetraose Based on a Crystal Soaked with Maltohexaose. | |||||||||
Components | NEOPULLULANASE | |||||||||
Keywords | HYDROLASE / pullulan / cyclodextrin / neopullulanase / maltohexaose / maltotetraose | |||||||||
Function / homology | Function and homology information neopullulanase / neopullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermoactinomyces vulgaris (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å | |||||||||
Authors | Yokota, T. / Tonozuka, T. / Shimura, Y. / Ichikawa, K. / Kamitori, S. / Sakano, Y. | |||||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2001 Title: Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues. Authors: Yokota, T. / Tonozuka, T. / Shimura, Y. / Ichikawa, K. / Kamitori, S. / Sakano, Y. #1: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2000 Title: Analysis of catalytic residues of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) by site-directed mutagenesis. Authors: Ichikawa, K. / Tonozuka, T. / Yokota, T. / Shimura, Y. / Sakano, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jib.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jib.ent.gz | 195.5 KB | Display | PDB format |
PDBx/mmJSON format | 1jib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jib_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1jib_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1jib_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 1jib_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1jib ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1jib | HTTPS FTP |
-Related structure data
Related structure data | 1jl8C 1bvzS 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: 67553.125 Da / Num. of mol.: 2 / Mutation: D325N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Plasmid: pTND325N / Production host: Escherichia coli (E. coli) / Strain (production host): MV1184 / References: UniProt: Q08751, neopullulanase #2: Polysaccharide | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.01 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG6000, MES, CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→39.6 Å / Num. all: 107522 / Num. obs: 22140 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 17.765 Å2 / Rmerge(I) obs: 0.154 / Rsym value: 0.137 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 3.3→3.48 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.269 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 107522 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BVZ Resolution: 3.3→39.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4478384.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.4191 Å2 / ksol: 0.284988 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.3→39.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.51 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 39.6 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.212 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 33.4 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.361 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.245 |