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Yorodumi- PDB-8k7h: Crystal structure of human lysosomal alpha-galactosidase A in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k7h | |||||||||
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Title | Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R)-2-(hydroxymethyl)-1-methylpyrrolidine-3,4-diol | |||||||||
Components | Alpha-galactosidase A | |||||||||
Keywords | HYDROLASE / alpha-galactosidase / glycosidase / iminosugar | |||||||||
Function / homology | Function and homology information glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | |||||||||
Authors | Li, H.Y. / Huang, K.F. / Ko, T.P. / Cheng, W.C. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Jacs Au / Year: 2024 Title: Mechanistic Insights into Dibasic Iminosugars as pH-Selective Pharmacological Chaperones to Stabilize Human alpha-Galactosidase. Authors: Li, H.Y. / Lin, H.Y. / Chang, S.K. / Chiu, Y.T. / Hou, C.C. / Ko, T.P. / Huang, K.F. / Niu, D.M. / Cheng, W.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k7h.cif.gz | 421.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k7h.ent.gz | 285.8 KB | Display | PDB format |
PDBx/mmJSON format | 8k7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k7h_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8k7h_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8k7h_validation.xml.gz | 35.3 KB | Display | |
Data in CIF | 8k7h_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/8k7h ftp://data.pdbj.org/pub/pdb/validation_reports/k7/8k7h | HTTPS FTP |
-Related structure data
Related structure data | 8k7dC 8k7eC 8k7fC 8k7gC 8k7iC 8k7jC 8k7kC 8k7lC 1r47S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: ens_1
NCS oper: (Code: givenMatrix: (-0.975231035545, 0.217691585345, 0.0391765360797), (0.217050516547, 0.907755019923, 0.358984535979), (0.0425852154621, 0.35859614816, -0.932520939148)Vector: -88. ...NCS oper: (Code: given Matrix: (-0.975231035545, 0.217691585345, 0.0391765360797), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45394.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Production host: Homo sapiens (human) / References: UniProt: P06280, alpha-galactosidase |
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-Sugars , 3 types, 6 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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 #4: Sugar | |
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-Non-polymers , 3 types, 544 molecules
#5: Chemical | Mass: 147.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO3 / Feature type: SUBJECT OF INVESTIGATION #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.82 Å3/Da / Density % sol: 56.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→30 Å / Num. obs: 47648 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 30.79 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.28→2.36 Å / Rmerge(I) obs: 0.867 / Num. unique obs: 4650 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R47 Resolution: 2.28→29.63 Å / SU ML: 0.2573 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8902 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.28→29.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 2.17418734545 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -43.1078374935 Å / Origin y: 21.4739806166 Å / Origin z: -22.3569636398 Å
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Refinement TLS group | Selection details: all |