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Yorodumi- PDB-3gh5: Crystal structure of beta-hexosaminidase from Paenibacillus sp. T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gh5 | ||||||
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Title | Crystal structure of beta-hexosaminidase from Paenibacillus sp. TS12 in complex with GlcNAc | ||||||
Components | beta-hexosaminidaseHexosaminidase | ||||||
Keywords | HYDROLASE / beta-N-acetylhexosaminidase / glycosphingolipids / Paenibacillus sp. / GH20 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / N-acetyl-beta-D-galactosaminidase activity / ganglioside catabolic process / beta-N-acetylglucosaminidase activity / lysosome / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | Paenibacillus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sumida, T. / Ishii, R. / Yanagisawa, T. / Yokoyama, S. / Ito, M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Molecular cloning and crystal structural analysis of a novel beta-N-acetylhexosaminidase from Paenibacillus sp. TS12 capable of degrading glycosphingolipids Authors: Sumida, T. / Ishii, R. / Yanagisawa, T. / Yokoyama, S. / Ito, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gh5.cif.gz | 225 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gh5.ent.gz | 176.5 KB | Display | PDB format |
PDBx/mmJSON format | 3gh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/3gh5 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/3gh5 | HTTPS FTP |
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-Related structure data
Related structure data | 3gh4C 3gh7C 1hp4S 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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Unit cell |
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-Components
#1: Protein | Mass: 57566.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paenibacillus sp. (bacteria) / Strain: TS12 / Gene: Hex1 / Plasmid: pET28c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: D0VX21*PLUS, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-SO4 / |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
Sequence details | A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE AUTHOR HAS SUBMITTED ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE AUTHOR HAS SUBMITTED TO DDBJ, ACCESSION NUMBER AB490155. THE RESIDUES (-22)- 0 ARE EXPRESSION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Na-Acetate, PEG2000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 19, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 68795 / % possible obs: 99.4 % / Redundancy: 6.9 % / Rsym value: 0.143 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.471 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB 1HP4 Resolution: 1.6→42.61 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.847 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 12.143 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→42.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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