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Yorodumi- PDB-5ndx: The bacterial orthologue of Human a-L-iduronidase does not need N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ndx | ||||||||||||
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Title | The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I | ||||||||||||
Components | Glycosyl hydrolase | ||||||||||||
Keywords | HYDROLASE / Human a-L-iduronidase / Mucopolysaccharidosis I / Catalytic itinerary / Reaction coordinates / Catalytic mechanism / N-glycosylation site / Rhizobium leguminosarum / Iduronidase | ||||||||||||
Function / homology | Function and homology information hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process Similarity search - Function | ||||||||||||
Biological species | Rhizobium leguminosarum bv. trifolii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||||||||
Authors | Raich, L. / Valero-Gonzalez, J. / Castro-Lopez, J. / Millan, C. / Jimenez-Garcia, M.J. / Nieto, P. / Uson, I. / Hurtado-Guerrero, R. / Rovira, C. | ||||||||||||
Funding support | Spain, 3items
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Citation | Journal: To Be Published Title: The bacterial orthologue of Human a-L-iduronidase does not need N-glycan post-translational modifications to be catalytically competent: Crystallography and QM/MM insights into Mucopolysaccharidosis I. Authors: Raich, L. / Valero-Gonzalez, J. / Castro-Lopez, J. / Millan, C. / Jimenez-Garcia, M.J. / Nieto, P. / Uson, I. / Hurtado-Guerrero, R. / Rovira, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ndx.cif.gz | 257.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ndx.ent.gz | 206.8 KB | Display | PDB format |
PDBx/mmJSON format | 5ndx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ndx_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5ndx_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5ndx_validation.xml.gz | 28.9 KB | Display | |
Data in CIF | 5ndx_validation.cif.gz | 42.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/5ndx ftp://data.pdbj.org/pub/pdb/validation_reports/nd/5ndx | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 68879.070 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: This enzyme is the inactive mutant Glu146Gln of Rhizobium leguminosarum Iduronidase Source: (gene. exp.) Rhizobium leguminosarum bv. trifolii (bacteria) Gene: BAE36_24485 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B8R7L2 | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1 M succinic acid, 1% PEG 2000 MME and 100 mM HEPES pH 7 |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 30, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 70222 / % possible obs: 99.9 % / Redundancy: 22.2 % / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.013 / Net I/σ(I): 38.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 22.5 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 5.6 / Rpim(I) all: 0.137 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: See our manuscript for the template Resolution: 2.2→149.85 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.414 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.108 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.533 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→149.85 Å
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Refine LS restraints |
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