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Yorodumi- PDB-7eiq: Crystal structure of chondroitin ABC lyase I in complex with chon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eiq | ||||||
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Title | Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 4S | ||||||
Components | Chondroitin sulfate ABC endolyase | ||||||
Keywords | LYASE / Polysaccharide lyase family 8 / carbohydrate binding | ||||||
Function / homology | Function and homology information chondroitin-sulfate-ABC endolyase / chondroitin-sulfate-ABC endolyase activity / glycosaminoglycan catabolic process / carbohydrate binding / carbohydrate metabolic process / periplasmic space / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Proteus vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Takashima, M. / Miyanaga, A. / Eguchi, T. | ||||||
Citation | Journal: Glycobiology / Year: 2021 Title: Substrate specificity of Chondroitinase ABC I based on analyses of biochemical reactions and crystal structures in complex with disaccharides. Authors: Takashima, M. / Watanabe, I. / Miyanaga, A. / Eguchi, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7eiq.cif.gz | 409.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eiq.ent.gz | 331.3 KB | Display | PDB format |
PDBx/mmJSON format | 7eiq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eiq_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7eiq_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7eiq_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 7eiq_validation.cif.gz | 67.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7eiq ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7eiq | HTTPS FTP |
-Related structure data
Related structure data | 7eipC 7eirC 7eisC 1hn0S 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
#1: Protein | Mass: 115216.391 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Proteus vulgaris (bacteria) References: UniProt: P59807, chondroitin-sulfate-ABC endolyase | ||||||
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#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.91 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: magnesium acetate, ammonium acetate, polyethylene glycol 3350, HEPES-Na |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 7, 2020 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 100438 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.101 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2 / Num. unique obs: 4953 / CC1/2: 0.711 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HN0 Resolution: 1.8→49.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.812 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: U VALUES : WITH TLS ADDED 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 max: 82.59 Å2 / Biso mean: 27.233 Å2 / Biso min: 11.07 Å2
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Refinement step | Cycle: final / Resolution: 1.8→49.05 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.587 Å / Origin y: 25.144 Å / Origin z: -31.967 Å
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