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Yorodumi- PDB-5x2i: Polygalacturonate Lyase by Fusing with a Self-assembling Amphipat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5x2i | ||||||
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Title | Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide | ||||||
Components | Pectate lyase | ||||||
Keywords | LYASE / tag-fusion enzyme / protein stability / hydrophobic force | ||||||
Function / homology | Function and homology information pectate lyase / pectate lyase activity / pectin catabolic process / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.05 Å | ||||||
Authors | Zhao, W.X. | ||||||
Funding support | China, 1items
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Citation | Journal: To be published Title: Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide Authors: Zhao, W.X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5x2i.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x2i.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x2i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/5x2i ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x2i | HTTPS FTP |
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-Related structure data
Related structure data | 1bn8S S: Starting model for refinement |
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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
#1: Protein | Mass: 43445.191 Da / Num. of mol.: 1 / Fragment: UNP residues 22-420 Source method: isolated from a genetically manipulated source Details: AEAEAKAKAEAEAKAK was the Self-assembling Amphipathic PeptideWISPTPPTTPTPPTTPTPTPAMD was the linker peptide. Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Strain: 168 / Gene: pel, BSU07560 / Production host: Escherichia coli (E. coli) / References: UniProt: P39116, pectate lyase |
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#2: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-CL / |
#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: 2.2 Å3/Da / Density % sol: 44.19 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.5 Details: 0.2 M sodium bromide, 20 mM Glycine-NaOH, 20 % polyethylene glycol 3350, 7 mM calcium chloride, 20 % glycerol PH range: 7.2-7.8 |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SACLA / Beamline: BL3 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Dec 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.86→28.427 Å / Num. obs: 18202 / % possible obs: 91.8 % / Redundancy: 2.3 % / Net I/σ(I): 12.1 |
-Processing
Software | Name: REFMAC / Version: 5.8.0135 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1BN8 Resolution: 2.05→28.427 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.411 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.187 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.746 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→28.427 Å
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Refine LS restraints |
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