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Yorodumi- PDB-4p5y: Structure of CBM32-3 from a family 31 glycoside hydrolase from Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p5y | ||||||
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Title | Structure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens in complex with N-acetylgalactosamine | ||||||
Components | Glycosyl hydrolase, family 31/fibronectin type III domain proteinGlycoside hydrolase | ||||||
Keywords | SUGAR BINDING PROTEIN / B-sandwich / carbohydrate-binding / N-acetylgalactosamine | ||||||
Function / homology | Function and homology information polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridium perfringens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Grondin, J.M. / Allingham, J.S. / Boraston, A.B. / Smith, S.P. | ||||||
Funding support | Canada, 1items
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Citation | Journal: PLoS ONE / Year: 2017 Title: Diverse modes of galacto-specific carbohydrate recognition by a family 31 glycoside hydrolase from Clostridium perfringens. Authors: Grondin, J.M. / Duan, D. / Kirlin, A.C. / Abe, K.T. / Chitayat, S. / Spencer, H.L. / Spencer, C. / Campigotto, A. / Houliston, S. / Arrowsmith, C.H. / Allingham, J.S. / Boraston, A.B. / Smith, S.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p5y.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p5y.ent.gz | 32.5 KB | Display | PDB format |
PDBx/mmJSON format | 4p5y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/4p5y ftp://data.pdbj.org/pub/pdb/validation_reports/p5/4p5y | HTTPS FTP |
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-Related structure data
Related structure data | 4lksSC 4lplC 4lqrC 4uapC 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: 18993.844 Da / Num. of mol.: 1 / Fragment: UNP residues 1640-1785 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / NCTC 8237 / Type A / Gene: CPF_1301 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0TRJ3, UniProt: A0A0H2YST8*PLUS |
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#2: Sugar | ChemComp-NGA / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.4M ammonium citrate |
-Data collection
Diffraction | Mean temperature: 93.15 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→42.89 Å / Num. obs: 5836 / % possible obs: 100 % / Redundancy: 6 % / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.5→2.6 Å / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: (PHENIX.REFINE: 1.8.4_1496) / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LKS Resolution: 2.5→42.89 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.89 Å
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Refine LS restraints |
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LS refinement shell |
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