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Yorodumi- PDB-4kh2: Crystal structure of human alpha-L-iduronidase complex with 2-deo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kh2 | |||||||||
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Title | Crystal structure of human alpha-L-iduronidase complex with 2-deoxy-2-fluoro-alpha-L-idopyranosyluronic acid fluoride | |||||||||
Components | Alpha-L-iduronidase | |||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / glycoside hydrolase family 39 / TIM barrel / beta sandwich / fibronectin III domain / glycosaminoglycans / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
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: 2.36 Å | |||||||||
Authors | Bie, H. / Yin, J. / He, X. / Kermode, A.R. / Goddard-Borger, E.D. / Withers, S.G. / James, M.N.G. | |||||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2013 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kh2.cif.gz | 263.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kh2.ent.gz | 209.5 KB | Display | PDB format |
PDBx/mmJSON format | 4kh2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kh2_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 4kh2_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 4kh2_validation.xml.gz | 45 KB | Display | |
Data in CIF | 4kh2_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/4kh2 ftp://data.pdbj.org/pub/pdb/validation_reports/kh/4kh2 | HTTPS FTP |
-Related structure data
Related structure data | 4kgjC 4kglC 4mj2C 4mj4C 4jxo C: citing same article (ref.) 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 | #7: Sugar | |
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-Non-polymers , 5 types, 233 molecules
#6: Chemical | ChemComp-GOL / #8: Chemical | #9: Chemical | ChemComp-TLA / | #10: Chemical | ChemComp-SRT / | #11: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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Sequence details | H33Q, Q63P, AND R105Q ARE NATURAL VARIANTS. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.5 % |
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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: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
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: 2.36→41.72 Å / Num. all: 73285 / Num. obs: 71893 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.204 / Net I/σ(I): 8.94 |
Reflection shell | Resolution: 2.36→2.42 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 1.64 / Rsym value: 0.8 / % possible all: 89.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4JXO 4jxo Resolution: 2.36→41.72 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.896 / SU B: 9.431 / SU ML: 0.216 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.243 / 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: 37.324 Å2
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Refinement step | Cycle: LAST / Resolution: 2.36→41.72 Å
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Refine LS restraints |
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