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Yorodumi- PDB-5xqo: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Pe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xqo | |||||||||
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Title | Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with tetrameric substrate | |||||||||
Components | Pcrglx protein | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 5xqo.cif.gz | 364.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xqo.ent.gz | 287.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xqo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xqo_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5xqo_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5xqo_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 5xqo_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/5xqo ftp://data.pdbj.org/pub/pdb/validation_reports/xq/5xqo | HTTPS FTP |
-Related structure data
Related structure data | 5xq3SC 5xqgC 5xqjC 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: 100806.484 Da / Num. of mol.: 2 / Fragment: UNP residues 22-927 / Mutation: Y458F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS #2: Polysaccharide | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-alpha-D- ...2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-2)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-alpha-L-rhamnopyranose-(1-4)-alpha-D- ...2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid-(1-3)-alpha-L-rhamnopyranose-(1-4)-alpha-D-galactopyranuronic acid-(1-2)-alpha-L-rhamnopyranose | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 3.1M Sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 26, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→119.58 Å / Num. obs: 40427 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 31.4 |
Reflection shell | Resolution: 3.2→3.26 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 4.83 / Num. unique obs: 1960 / CC1/2: 0.921 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XQ3 Resolution: 3.2→119.58 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.889 / SU B: 23.861 / SU ML: 0.39 / Cross valid method: THROUGHOUT / ESU R Free: 0.524 / 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: 86.804 Å2
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Refinement step | Cycle: 1 / Resolution: 3.2→119.58 Å
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Refine LS restraints |
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