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Yorodumi- PDB-5xq3: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xq3 | ||||||
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Title | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum | ||||||
Components | (Pcrglx protein) x 2 | ||||||
Keywords | LYASE / exo-rhamnogalacturonan lyase / enzyme / pectin / SAD / Se | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Penicillium chrysogenum (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å | ||||||
Authors | Kunishige, Y. / Iwai, M. / Tada, T. / Nishimura, S. / Sakamoto, T. | ||||||
Citation | Journal: FEBS Lett. / Year: 2018 Title: Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26 Authors: Kunishige, Y. / Iwai, M. / Nakazawa, M. / Ueda, M. / Tada, T. / Nishimura, S. / Sakamoto, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xq3.cif.gz | 356.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xq3.ent.gz | 291.3 KB | Display | PDB format |
PDBx/mmJSON format | 5xq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xq3_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
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Full document | 5xq3_full_validation.pdf.gz | 459.2 KB | Display | |
Data in XML | 5xq3_validation.xml.gz | 58.6 KB | Display | |
Data in CIF | 5xq3_validation.cif.gz | 81.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/5xq3 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/5xq3 | HTTPS FTP |
-Related 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: 101064.758 Da / Num. of mol.: 1 / Fragment: UNP residues 22-927 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS | ||
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#2: Protein | Mass: 100822.484 Da / Num. of mol.: 1 / Fragment: UNP residues 22-927 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS | ||
#3: Chemical | #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: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.9 M Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Oct 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→120.09 Å / Num. obs: 57725 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 33 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 15 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2860 / CC1/2: 0.886 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.85→120.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.05 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.539 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→120.09 Å
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Refine LS restraints |
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