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Yorodumi- PDB-4obr: Crystal structure of human alpha-L-iduronidase complex with alpha... -
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-Basic information
Entry | Database: PDB / ID: 4obr | |||||||||
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Title | Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid | |||||||||
Components | Alpha-L-iduronidase | |||||||||
Keywords | HYDROLASE / glycoside hydrolase family 39 / TIM barrel / beta sandwich / fibronectin III domain / glycosaminoglycans | |||||||||
Function / homology | Function and homology information L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation ...L-iduronidase / L-iduronidase activity / disaccharide metabolic process / MPS I - Hurler syndrome / heparin catabolic process / dermatan sulfate catabolic process / glycosaminoglycan catabolic process / CS/DS degradation / heparan sulfate proteoglycan catabolic process / HS-GAG degradation / lysosomal lumen / signaling receptor binding / extracellular exosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | |||||||||
Authors | Bie, H.Y. / Yin, J. / He, X. / Kermode, A.R. / James, M.N.G. | |||||||||
Citation | Journal: To be Published Title: Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid Authors: Bie, H.Y. / Yin, J. / He, X. / Kermode, A.R. / James, M.N.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4obr.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4obr.ent.gz | 208.6 KB | Display | PDB format |
PDBx/mmJSON format | 4obr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4obr_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4obr_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4obr_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 4obr_validation.cif.gz | 60.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ob/4obr ftp://data.pdbj.org/pub/pdb/validation_reports/ob/4obr | HTTPS FTP |
-Related structure data
Related structure data | 4mj2S 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 70053.320 Da / Num. of mol.: 2 / Fragment: UNP residues 27-653 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IDUA / Plasmid: pARC5s3 / Production host: Arabidopsis thaliana (thale cress) / Strain (production host): cgl1 1 / References: UniProt: P35475, L-iduronidase |
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-Sugars , 5 types, 8 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | #8: Sugar | |
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-Non-polymers , 5 types, 121 molecules
#6: Chemical | ChemComp-GOL / #7: Chemical | #9: Chemical | #10: Chemical | ChemComp-SO4 / | #11: Water | ChemComp-HOH / | |
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-Details
Sequence details | H33Q, Q63P, AND R105Q ARE NATURAL VARIANTS. |
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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: 3.29 Å3/Da / Density % sol: 62.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.01 M HEPES, pH 7.5, 0.26 M sodium potassium tartrate, 20% PEG3350, 50 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Jun 3, 2013 Details: collimating mirror with two stripes (Si, Rh/Pt) and toroidal focusing mirror (Rh/Pt) |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→48.94 Å / Num. all: 64924 / Num. obs: 63496 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.085 / Net I/σ(I): 12.89 |
Reflection shell | Resolution: 2.46→2.524 Å / Redundancy: 2.82 % / Mean I/σ(I) obs: 3.43 / Rsym value: 0.389 / % possible all: 82.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4MJ2 Resolution: 2.46→48.94 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.044 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.247 / 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: 39.549 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→48.94 Å
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Refine LS restraints |
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