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Yorodumi- PDB-4lks: Structure of CBM32-3 from a family 31 glycoside hydrolase from Cl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lks | ||||||
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Title | Structure of CBM32-3 from a family 31 glycoside hydrolase from Clostridium perfringens in complex with galactose | ||||||
Components | Glycosyl hydrolase, family 31/fibronectin type III domain protein | ||||||
Keywords | SUGAR BINDING PROTEIN / B-sandwich / carbohydrate-binding / galactose | ||||||
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: 1.5 Å | ||||||
Authors | Grondin, J.M. / Duan, D. / Kirlin, A.C. / Furness, H.S. / 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 | 4lks.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lks.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 4lks.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lk/4lks ftp://data.pdbj.org/pub/pdb/validation_reports/lk/4lks | HTTPS FTP |
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-Related structure data
Related structure data | 4lplC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18993.844 Da / Num. of mol.: 2 / Fragment: CBM32-3, 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 #2: Chemical | #3: Sugar | #4: 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: 1.95 Å3/Da / Density % sol: 36.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6M ammonium citrate, 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: NSLS / Beamline: X6A / Wavelength: 0.98 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si (III) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→40 Å / Num. obs: 53421 / % possible obs: 98.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.051 / Χ2: 1.236 / Net I/σ(I): 16.4 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.5→30.659 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8808 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 18.55 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.324 Å2 / ksol: 0.394 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 69.66 Å2 / Biso mean: 16.3428 Å2 / Biso min: 5.62 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.659 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19
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