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Yorodumi- PDB-6j33: Crystal structure of ligand-free of PulA from Klebsiella pneumoniae -
+Open data
-Basic information
Entry | Database: PDB / ID: 6j33 | ||||||
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Title | Crystal structure of ligand-free of PulA 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: 1.297 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 | 6j33.cif.gz | 1005 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j33.ent.gz | 826.2 KB | Display | PDB format |
PDBx/mmJSON format | 6j33.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6j33_validation.pdf.gz | 460.3 KB | Display | wwPDB validaton report |
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Full document | 6j33_full_validation.pdf.gz | 478.1 KB | Display | |
Data in XML | 6j33_validation.xml.gz | 103 KB | Display | |
Data in CIF | 6j33_validation.cif.gz | 165 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/6j33 ftp://data.pdbj.org/pub/pdb/validation_reports/j3/6j33 | HTTPS FTP |
-Related structure data
Related structure data | 6j34C 6j35C 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: 114462.711 Da / Num. of mol.: 2 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 | ChemComp-ACT / #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: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.2M Magnesium acetate, 0.2M Sodium Acetate buffer (pH 6.0), 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: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.297→50 Å / Num. obs: 495665 / % possible obs: 94.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.026 / Rrim(I) all: 0.058 / Net I/av σ(I): 0.201 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.3→1.34 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 46251 / CC1/2: 0.849 / Rpim(I) all: 0.24 / Rrim(I) all: 0.413 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2FHF Resolution: 1.297→39.264 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 15.53 / 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: 1.297→39.264 Å
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Refine LS restraints |
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LS refinement shell |
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