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Yorodumi- PDB-6j35: Crystal structure of ligand-free of PulA-G680L mutant from Klebsi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j35 | ||||||
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Title | Crystal structure of ligand-free of PulA-G680L mutant from Klebsiella pneumoniae | ||||||
Components | Pullulanase | ||||||
Keywords | HYDROLASE / Pullulanase / Klebsiella pneumoniae / ligand-free / G680 | ||||||
Function / homology | Function and homology information pullulanase / pullulanase activity / carbohydrate binding / carbohydrate metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.839 Å | ||||||
Authors | Saka, N. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Relationship between the induced-fit loop and the activity of Klebsiella pneumoniae pullulanase. Authors: Saka, N. / Malle, D. / Iwamoto, H. / Takahashi, N. / Mizutani, K. / Mikami, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j35.cif.gz | 451.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j35.ent.gz | 356.7 KB | Display | PDB format |
PDBx/mmJSON format | 6j35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j35 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j35 | HTTPS FTP |
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-Related structure data
Related structure data | 6j33C 6j34C 6j4hC 2fhfS 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: 114518.805 Da / Num. of mol.: 2 / Mutation: G680L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: pulA / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: W9BQ28 #2: Chemical | ChemComp-MG / #3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | Sequence details | N229S was due to spontaneous mutation. | |
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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: 2.38 Å3/Da / Density % sol: 48.32 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M sodium acetate buffer (pH 6.0), 0.2M magnesium acetate, 20%(w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Apr 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.839→50 Å / Num. obs: 181784 / % possible obs: 97.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 16 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.037 / Rrim(I) all: 0.06 / Net I/av σ(I): 19.7 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.84→1.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 8.8 / Num. unique obs: 17267 / CC1/2: 0.968 / Rpim(I) all: 0.107 / Rrim(I) all: 0.175 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHF Resolution: 1.839→38.721 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.839→38.721 Å
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Refine LS restraints |
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LS refinement shell |
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