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Yorodumi- PDB-4eib: Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4eib | ||||||
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Title | Crystal Structure of Circular Permuted CBM21 (CP90) Gives Insight into the Altered Selectivity on Carbohydrate Binding. | ||||||
Components | GlucoamylaseGlucan 1,4-a-glucosidase | ||||||
Keywords | HYDROLASE / BETA BARREL / Starch Binding / Amylose | ||||||
Function / homology | Function and homology information polysaccharide metabolic process / glucan 1,4-alpha-glucosidase / glucan 1,4-alpha-glucosidase activity / fungal-type vacuole / metal ion binding Similarity search - Function | ||||||
Biological species | Rhizopus oryzae (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å | ||||||
Authors | Stephen, P. / Cheng, K.C. / Lyu, P.C. | ||||||
Citation | Journal: Plos One / Year: 2012 Title: Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites Authors: Stephen, P. / Cheng, K.C. / Lyu, P.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4eib.cif.gz | 106 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eib.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 4eib.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ei/4eib ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eib | HTTPS FTP |
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-Related structure data
Related structure data | 2v8lS 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 12063.118 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 115-131, 26-114 Source method: isolated from a genetically manipulated source Details: CIRCULAR PERMUTED GLUCOAMYLASE OF RESIDUES 115-131 AND RESIDUES 26-114. Source: (gene. exp.) Rhizopus oryzae (fungus) / Gene: amyA, CBM21 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B7XC04 |
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-Non-polymers , 6 types, 127 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-NH4 / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | HIS19 AND MET20 WERE USED IN THE CIRCULAR PERMUTATIO |
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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: 2.06 Å3/Da / Density % sol: 40.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 1.26M (NH4)2SO4, 0.1M acetate pH 4.5, 0.2M NaCl , VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 14, 2011 Details: Vertically Focusing Mirror, Horizontally Focusing Single Crystal Si(111) Bent Monochromator |
Radiation | Monochromator: Horizontally Focusing Single Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 1.8285→66.94 Å / Num. obs: 14988 / % possible obs: 99.8 % / Redundancy: 7.5 % / Biso Wilson estimate: 16.65 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 49.4 |
Reflection shell | Resolution: 1.86→1.89 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.038 / Mean I/σ(I) obs: 13.69 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2V8L Resolution: 1.86→24.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.92 / SU B: 7.254 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 mean: 19.865 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→24.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.861→1.909 Å / Total num. of bins used: 20
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