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Yorodumi- PDB-3wdj: Crystal structure of Pullulanase complexed with maltotetraose fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wdj | |||||||||
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Title | Crystal structure of Pullulanase complexed with maltotetraose from Anoxybacillus sp. LM18-11 | |||||||||
Components | Type I pullulanase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase / pullulanase | |||||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / carbohydrate metabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Anoxybacillus sp. LM18-11 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | |||||||||
Authors | Xu, J. / Ren, F. / Huang, C.H. / Zheng, Y. / Zhen, J. / Ko, T.P. / Chen, C.C. / Chan, H.C. / Guo, R.T. / Ma, Y. / Song, H. | |||||||||
Citation | Journal: To be Published Title: Cloning, Expression, Functional and Structural Studies of Pullulanase from Anoxybacillus sp. LM18-11 Authors: Xu, J. / Ren, F. / Huang, C.H. / Zheng, Y. / Zhen, J. / Chen, C.C. / Chan, H.C. / Guo, R.T. / Ma, Y. / Song, H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wdj.cif.gz | 171.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wdj.ent.gz | 133 KB | Display | PDB format |
PDBx/mmJSON format | 3wdj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/3wdj ftp://data.pdbj.org/pub/pdb/validation_reports/wd/3wdj | HTTPS FTP |
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-Related structure data
Related structure data | 3wdhSC 3wdiC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 82172.422 Da / Num. of mol.: 1 / Fragment: UNP residues 3-707 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anoxybacillus sp. LM18-11 (bacteria) / Gene: pulA / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: K9L0H1, pullulanase | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltotetraose #3: Chemical | ChemComp-CA / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.81 % |
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Crystal grow | Temperature: 295 K / pH: 7.5 Details: 0.1M HEPES, pH 7.5, 7%(w/v) Polyethylene Glycol 8000, 10%(v/v) Ethylene Glycol , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→25 Å / Num. obs: 42431 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 4.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WDH Resolution: 2.22→25 Å / Cross valid method: RANDOM / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.22→25 Å
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LS refinement shell | Resolution: 2.22→2.3 Å /
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