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Yorodumi- PDB-4lpl: Structure of CBM32-1 from a family 31 glycoside hydrolase from Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lpl | ||||||
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Title | Structure of CBM32-1 from a family 31 glycoside hydrolase from Clostridium perfringens | ||||||
Components | Glycosyl hydrolase, family 31/fibronectin type III domain protein | ||||||
Keywords | SUGAR BINDING PROTEIN / B-sandwich / carbohydrate-binding | ||||||
Function / homology | Function and homology information alpha-glucosidase activity / N-glycan processing / 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: 1.35 Å | ||||||
Authors | Grondin, J.M. / Duan, D. / Heather, F.S. / Spencer, C.A. / Allingham, J.S. / Smith, S.P. | ||||||
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 | 4lpl.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lpl.ent.gz | 30.9 KB | Display | PDB format |
PDBx/mmJSON format | 4lpl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lpl_validation.pdf.gz | 420.6 KB | Display | wwPDB validaton report |
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Full document | 4lpl_full_validation.pdf.gz | 420.6 KB | Display | |
Data in XML | 4lpl_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4lpl_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/4lpl ftp://data.pdbj.org/pub/pdb/validation_reports/lp/4lpl | HTTPS FTP |
-Related structure data
Related structure data | 4lksC 4lqrC 4p5yC 4uapC 2j1aS C: citing same article (ref.) S: Starting model for refinement |
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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: 20996.625 Da / Num. of mol.: 1 / Fragment: CBM32-1, UNP residues 935-1095 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: Chemical | ChemComp-CA / |
#3: Chemical | ChemComp-MG / |
#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: 1.93 Å3/Da / Density % sol: 35.9 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 32% PEG 4000, 225mM MgCl2 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93.15 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 16, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (III) double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.35→30 Å / Num. obs: 30335 / % possible obs: 98.9 % / Redundancy: 11 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J1A Resolution: 1.35→23.637 Å / Occupancy max: 1 / Occupancy min: 0.01 / SU ML: 0.12 / σ(F): 0.1 / Phase error: 19.85 / 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 / Bsol: 40.474 Å2 / ksol: 0.399 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 43.8 Å2 / Biso mean: 16.0366 Å2 / Biso min: 6.37 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→23.637 Å
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Refine LS restraints |
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LS refinement shell |
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