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- PDB-5j7z: Crystal structure of endoglycoceramidase I from Rhodococ-cus equi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j7z | ||||||||||||
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Title | Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1 | ||||||||||||
![]() | Putative secreted endoglycosylceramidase | ||||||||||||
![]() | HYDROLASE / Complex | ||||||||||||
Function / homology | ![]() endoglycosylceramidase / endoglycosylceramidase activity / galactosylceramide catabolic process / extracellular region / membrane Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Chen, L. | ||||||||||||
![]() | ![]() Title: Structural Insights into the Broad Substrate Specificity of a Novel Endoglycoceramidase I Belonging to a New Subfamily of GH5 Glycosidases. Authors: Han, Y.B. / Chen, L.Q. / Li, Z. / Tan, Y.M. / Feng, Y. / Yang, G.Y. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 194.2 KB | Display | ![]() |
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PDB format | ![]() | 149 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 36.1 KB | Display | |
Data in CIF | ![]() | 52.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ccuSC ![]() 5j14C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53869.863 Da / Num. of mol.: 2 / Mutation: E339S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() Strain (production host): BL21-GOLD(DE3)PLYSS AG / References: UniProt: E4W8N9, UniProt: A0A3S5YBC7*PLUS #2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha- ...beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-18C / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.71 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop Details: PEG800 SODIUM HYDROXIDE AMMONIUM CHLORIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. obs: 55310 / % possible obs: 99.2 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.25 |
Reflection shell | Resolution: 2.15→2.23 Å / Rmerge(I) obs: 0.485 / Rpim(I) all: 0.269 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CCU Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.383 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.168 / 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: 24.94 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→50 Å
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Refine LS restraints |
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