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Yorodumi- PDB-7eir: Crystal structure of chondroitin ABC lyase I in complex with chon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7eir | ||||||
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Title | Crystal structure of chondroitin ABC lyase I in complex with chondroitin disaccharide 6S | ||||||
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: 1.92 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 | 7eir.cif.gz | 407.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7eir.ent.gz | 328.3 KB | Display | PDB format |
PDBx/mmJSON format | 7eir.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7eir_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7eir_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7eir_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 7eir_validation.cif.gz | 66.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/7eir ftp://data.pdbj.org/pub/pdb/validation_reports/ei/7eir | HTTPS FTP |
-Related structure data
Related structure data | 7eipC 7eiqC 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: Chemical | ChemComp-GOL / | #5: 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: 2.33 Å3/Da / Density % sol: 47.16 % |
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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: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 19, 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: 1.92→50 Å / Num. obs: 83417 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.128 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 1.92→1.96 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.846 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4522 / CC1/2: 0.746 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HN0 Resolution: 1.92→49.13 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.136 / 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: 102.96 Å2 / Biso mean: 33.049 Å2 / Biso min: 11.11 Å2
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Refinement step | Cycle: final / Resolution: 1.92→49.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.97 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -8.932 Å / Origin y: -25.432 Å / Origin z: 31.893 Å
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