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- PDB-4kgj: Crystal structure of human alpha-L-iduronidase complex with 5-flu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kgj | |||||||||
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Title | Crystal structure of human alpha-L-iduronidase complex with 5-fluoro-alpha-L-idopyranosyluronic acid fluoride | |||||||||
![]() | Alpha-L-iduronidase | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / glycoside hydrolase family 39 / TIM barrel / beta sandwich / fibronectin III domain / glycosaminoglycans / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bie, H. / Yin, J. / He, X. / Kermode, A.R. / Goddard-Borger, E.D. / Withers, S.G. / James, M.N.G. | |||||||||
![]() | ![]() Title: Insights into mucopolysaccharidosis I from the structure and action of alpha-L-iduronidase. Authors: Bie, H. / Yin, J. / He, X. / Kermode, A.R. / Goddard-Borger, E.D. / Withers, S.G. / James, M.N. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 255.6 KB | Display | ![]() |
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PDB format | ![]() | 204.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4kglC ![]() 4kh2C ![]() 4mj2C ![]() 4mj4C ![]() 4jxo 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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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.) ![]() ![]() ![]() |
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-Sugars , 5 types, 8 molecules ![](data/chem/img/NAG.gif)
![](data/chem/img/IDF.gif)
![](data/chem/img/IDF.gif)
#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 | #7: Sugar | |
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-Non-polymers , 4 types, 58 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/TLA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#6: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | ChemComp-CL / | #10: 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: ![]() |
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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, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2013 / Details: Rh coated flat mirror |
Radiation | Monochromator: Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→38.05 Å / Num. all: 36188 / Num. obs: 36079 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rsym value: 0.188 / Net I/σ(I): 11.75 |
Reflection shell | Resolution: 2.99→3.1 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.35 / Rsym value: 0.74 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4JXO ![]() 4jxo Resolution: 2.99→38.05 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / SU B: 15.091 / SU ML: 0.271 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 39.848 Å2
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Refinement step | Cycle: LAST / Resolution: 2.99→38.05 Å
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Refine LS restraints |
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