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- PDB-5xc2: Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xc2 | ||||||||||||
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Title | Crystal structure of GH family 81 beta-1,3-glucanase from Rhizomucr miehei complexed with laminarihexaose | ||||||||||||
![]() | Endo-beta-1,3-glucanase | ||||||||||||
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Function / homology | ![]() glucan endo-1,4-beta-glucanase activity, C-3 substituted reducing group / glucan endo-1,3-beta-glucanase activity, C-3 substituted reducing group / glucan endo-1,3-beta-D-glucosidase / glucan endo-1,3-beta-D-glucosidase activity / polysaccharide catabolic process / cell wall organization / extracellular region Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Qin, Z. / Yang, S. / Peng, Z. / Yan, Q. / Jiang, Z. | ||||||||||||
![]() | ![]() Title: Catalytic mechanism of glycoside hydrolase family 81 beta-1,3-glucanase Authors: Yang, S. / Qin, Z. / Zhou, P. / Yan, Q. / Jiang, Z. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 568.3 KB | Display | ![]() |
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PDB format | ![]() | 468.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5xbzC ![]() 4k3aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein / Non-polymers , 2 types, 483 molecules ABCD![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 89586.039 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() ![]() References: UniProt: A0A023I7E1, glucan endo-1,3-beta-D-glucosidase #7: Water | ChemComp-HOH / | ![]() |
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-Sugars , 5 types, 14 molecules
#2: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D- ...beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose![]() Source method: isolated from a genetically manipulated source | ||||||
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#3: Polysaccharide | ![]() Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-glucopyranose-(1-3)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose ![]() Source method: isolated from a genetically manipulated source #6: Polysaccharide | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.48 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: laminarihexaose (G6) was added to the protein solution at a final concentration of 1%(w/v). The complex crystals were obtained in a reservoir solution containing 24%(w/v) PEG4000, 80 mM Tris- ...Details: laminarihexaose (G6) was added to the protein solution at a final concentration of 1%(w/v). The complex crystals were obtained in a reservoir solution containing 24%(w/v) PEG4000, 80 mM Tris-HCl (pH 8.5), and 6%(v/v) MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Dec 12, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.7→50 Å / Num. obs: 74950 / % possible obs: 99.55 % / Redundancy: 17 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 2.7→2.94 Å / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 2.36 / % possible all: 99.16 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4k3a Resolution: 2.7→29.73 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.44 / 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: 2.7→29.73 Å
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Refine LS restraints |
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LS refinement shell |
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