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Yorodumi- PDB-8bdp: A GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bdp | ||||||
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Title | A GH20 family sulfoglycosidase Bt4394 in complex with NAG-thiazoline and sulfite | ||||||
Components | Beta-N-acetylhexosaminidaseHexosaminidase | ||||||
Keywords | HYDROLASE / intermediate complex / inhibitor / GH20 | ||||||
Function / homology | Function and homology information glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process / membrane Similarity search - Function | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å | ||||||
Authors | Zhang, Z. / He, Y. / Jin, Y. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bdp.cif.gz | 574.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bdp.ent.gz | 361.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bdp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/8bdp ftp://data.pdbj.org/pub/pdb/validation_reports/bd/8bdp | HTTPS FTP |
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-Related structure data
Related structure data | 7dupC 7dvaC 7dvbC 8balC 8bblC 3rcnS 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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-Components
#1: Protein | Mass: 61751.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Strain: ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50 Gene: BT_4394 / Production host: Escherichia coli (E. coli) / Strain (production host): RosettaTM(DE3)pLysS / References: UniProt: Q89ZI3, beta-N-acetylhexosaminidase |
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#2: Chemical | ChemComp-CL / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: PROTEIN STOCK AT 45 MG/ML IN THE REMARK 280 BUFFER OF 50 MM NAPO4 AND 500 MM NACL IS MIXED WITH THE REMARK 280 PRECIPITANT OF 0.2 M KSCN, 21% PEG3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 6. ...Details: PROTEIN STOCK AT 45 MG/ML IN THE REMARK 280 BUFFER OF 50 MM NAPO4 AND 500 MM NACL IS MIXED WITH THE REMARK 280 PRECIPITANT OF 0.2 M KSCN, 21% PEG3350, 0.1 M BIS-TRIS PROPANE REMARK 280 PH 6.5, AT A RATIO OF 1.2: 1. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979183 Å / Relative weight: 1 |
Reflection | Resolution: 1.47→70.63 Å / Num. obs: 91859 / % possible obs: 95.4 % / Redundancy: 1.9 % / CC1/2: 0.997 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.47→1.5 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 3088 / CC1/2: 0.624 / % possible all: 65 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3rcn Resolution: 1.47→70.628 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.199 / WRfactor Rwork: 0.142 / SU B: 3.759 / SU ML: 0.059 / Average fsc free: 0.9762 / Average fsc work: 0.9901 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.065 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.47→70.628 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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