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Yorodumi- PDB-5g2t: BT1596 in complex with its substrate 4,5 unsaturated uronic acid ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g2t | ||||||||||||
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Title | BT1596 in complex with its substrate 4,5 unsaturated uronic acid alpha 1,4 D-Glucosamine-2-N, 6-O-disulfate | ||||||||||||
Components | 2-O GLYCOSAMINOGLYCAN SULFATASE | ||||||||||||
Keywords | HYDROLASE / GLYCOSAMINOGLYCAN SULFATASE | ||||||||||||
Function / homology | Function and homology information glucuronate-2-sulfatase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / arylsulfatase activity / metal ion binding Similarity search - Function | ||||||||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||||||||
Authors | Cartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. ...Cartmell, A. / Lowe, E.C. / Basle, A. / Crouch, L.I. / Czjzek, M. / Turnbull, J. / Henrissat, B. / Terrapon, N. / Thomas, S. / Murray, H. / Firbank, S.J. / Bolam, D.N. | ||||||||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017 Title: How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Authors: Cartmell, A. / Lowe, E.C. / Basle, A. / Firbank, S.J. / Ndeh, D.A. / Murray, H. / Terrapon, N. / Lombard, V. / Henrissat, B. / Turnbull, J.E. / Czjzek, M. / Gilbert, H.J. / Bolam, D.N. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5g2t.cif.gz | 395.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2t.ent.gz | 321 KB | Display | PDB format |
PDBx/mmJSON format | 5g2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2t ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2t | HTTPS FTP |
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-Related structure data
Related structure data | 4ak1C 4ak2C 5g2uC 5g2vC 3b5qS 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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2 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54895.754 Da / Num. of mol.: 4 / Fragment: SULFATASE, UNP RESIDUE 13-481 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A7C8, EC: 3.1.6.18 |
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-Sugars , 2 types, 4 molecules
#2: Polysaccharide | Type: oligosaccharide / Mass: 577.470 Da / Num. of mol.: 2 / Source method: obtained synthetically #6: Sugar | |
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-Non-polymers , 4 types, 1213 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-CL / #7: Water | ChemComp-HOH / | |
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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: 2.26 Å3/Da / Density % sol: 45.56 % / Description: NONE |
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Crystal grow | Details: 14-20 % PEG 3350 0.2 M KCL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2014 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.4 Å / Num. obs: 153578 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.6 / % possible all: 76.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B5Q Resolution: 1.9→125.34 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.314 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
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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: 20.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→125.34 Å
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Refine LS restraints |
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