+Open data
-Basic information
Entry | Database: PDB / ID: 1o7a | |||||||||
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Title | Human beta-Hexosaminidase B | |||||||||
Components | BETA-HEXOSAMINIDASE BETA CHAIN | |||||||||
Keywords | HYDROLASE / GLYCOSYL HYDROLASE / HEXOSAMINIDASE / LYSOSOMAL / SPHINGOLIPID DEGRADATION / SANDHOFF DISEASE / BA8-BARREL / GLYCOSIDASE | |||||||||
Function / homology | Function and homology information beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / penetration of zona pellucida / CS/DS degradation / Hyaluronan uptake and degradation / male courtship behavior / cortical granule ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / penetration of zona pellucida / CS/DS degradation / Hyaluronan uptake and degradation / male courtship behavior / cortical granule / glycosaminoglycan metabolic process / acetylglucosaminyltransferase activity / astrocyte cell migration / beta-N-acetylhexosaminidase activity / hyaluronan catabolic process / maintenance of location in cell / phospholipid biosynthetic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / lipid storage / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / azurophil granule / oogenesis / lysosome organization / neuromuscular process controlling balance / single fertilization / myelination / lysosomal lumen / acrosomal vesicle / skeletal system development / locomotory behavior / sensory perception of sound / intracellular calcium ion homeostasis / neuron cellular homeostasis / azurophil granule lumen / regulation of cell shape / lysosome / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.25 Å | |||||||||
Authors | Maier, T. / Strater, N. / Schuette, C. / Klingenstein, R. / Sandhoff, K. / Saenger, W. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: The X-Ray Crystal Structure of Human Beta-Hexosaminidase B Provides New Insights Into Sandhoff Disease Authors: Maier, T. / Strater, N. / Schuette, C. / Klingenstein, R. / Sandhoff, K. / Saenger, W. #1: Journal: Glycobiology / Year: 2001 Title: Complete Analysis of the Glycosylation and Disulfide Bond Pattern of Human Beta-Hexosaminidase B by Maldi-Ms Authors: Schuette, C.G. / Weissgerber, J. / Sandhoff, K. #2: Journal: Protein Expr.Purif. / Year: 1990 Title: Synthesis of a Human Lysosomal Enzyme, Beta-Hexosaminidase B, Using the Baculaovirus Expression System Authors: Boose, J.A. / Tifft, C.J. / Proia, R.L. / Myerowitz, R. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1o7a.cif.gz | 630 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1o7a.ent.gz | 537.9 KB | Display | PDB format |
PDBx/mmJSON format | 1o7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1o7a_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1o7a_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 1o7a_validation.xml.gz | 135 KB | Display | |
Data in CIF | 1o7a_validation.cif.gz | 193.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/1o7a ftp://data.pdbj.org/pub/pdb/validation_reports/o7/1o7a | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 58925.711 Da / Num. of mol.: 6 / Fragment: 42-556 Source method: isolated from a genetically manipulated source Details: RECOMBINANTLY EXPRESSED FRAGMENT COMPOSED OF RESIDUES 42-556, N-TERMINUS OF MATURE HUMAN ENZYME IS BETWEEN RESIDUE 48 - 50 Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PACYM-1BETA / Cell line (production host): Sf21 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P07686, beta-N-acetylhexosaminidase |
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-Sugars , 3 types, 18 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-GDL / #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 2341 molecules
#5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Details
Compound details | BETA-HEXOSAMINIDASE IS RESPONSIBLE FOR THE DEGRADATION OF GM2 GANGLIOSIDES, AND A VARIETY OF OTHER ...BETA-HEXOSAMINI |
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Sequence details | EXPRESSED CONSTRUCT CONTAINS RESIDUES 42-TO 556 OF THE PRECURSOR PROTEIN |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 5.6 Details: HANGING DROP VAPOUR DIFFUSION PROTEIN SOLUTION: 10 MG/ML HEXB IN 10MM SODIUM CITRATE, 100 MM NACL, PH6.0 RESERVOIR SOLUTION: 100 MM SODIUM CITRATE, PH 5.6, 16% (V/V) ETHYLENE GLYCOL, 10%(V/V) ...Details: HANGING DROP VAPOUR DIFFUSION PROTEIN SOLUTION: 10 MG/ML HEXB IN 10MM SODIUM CITRATE, 100 MM NACL, PH6.0 RESERVOIR SOLUTION: 100 MM SODIUM CITRATE, PH 5.6, 16% (V/V) ETHYLENE GLYCOL, 10%(V/V) POLYETHYLENE GLYCOL 8000 | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 23, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 180325 / % possible obs: 99.9 % / Redundancy: 10.7 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 25.4 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5.5 / % possible all: 100 |
Reflection | *PLUS Highest resolution: 2.25 Å / Lowest resolution: 30 Å / Num. measured all: 1930354 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 5.5 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.25→28.12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4883320.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.6122 Å2 / ksol: 0.340616 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.25→28.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.33 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
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Xplor file |
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Refine LS restraints | *PLUS
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