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Yorodumi- PDB-5g2v: Structure of BT4656 in complex with its substrate D-Glucosamine-2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5g2v | |||||||||
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Title | Structure of BT4656 in complex with its substrate D-Glucosamine-2-N, 6-O-disulfate. | |||||||||
Components | N-ACETYLGLUCOSAMINE-6-SULFATASE | |||||||||
Keywords | HYDROLASE / GLYCOSAMINOGLYCAN SULFATASE | |||||||||
Function / homology | Function and homology information Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / hydrolase activity Similarity search - Function | |||||||||
Biological species | BACTEROIDES THETAIOTAOMICRON (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 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 | 5g2v.cif.gz | 234.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5g2v.ent.gz | 187.1 KB | Display | PDB format |
PDBx/mmJSON format | 5g2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5g2v_validation.pdf.gz | 768.6 KB | Display | wwPDB validaton report |
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Full document | 5g2v_full_validation.pdf.gz | 770.4 KB | Display | |
Data in XML | 5g2v_validation.xml.gz | 24.4 KB | Display | |
Data in CIF | 5g2v_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g2/5g2v ftp://data.pdbj.org/pub/pdb/validation_reports/g2/5g2v | HTTPS FTP |
-Related 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: 62340.828 Da / Num. of mol.: 1 / Fragment: ALPHA/BETA HYDROLASE FOLD, RESIDUES 45-558 Source method: isolated from a genetically manipulated source Details: D-GLUCOSAMINE-2-N, 6-O-DISULFATE Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria) Strain: VPI-5482 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q89YS5, EC: 3.1.6.14 |
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#2: Chemical | ChemComp-CA / |
#3: Sugar | ChemComp-SGN / |
#4: Chemical | ChemComp-NO3 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.16 % / Description: NONE |
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Crystal grow | Details: 20 % PEG 3350 0.2 M SODIUM NITRATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→47.5 Å / Num. obs: 101665 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 1.39→1.41 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.8 / % possible all: 99.4 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.39→58.65 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.183 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.041 / 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: 11.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.39→58.65 Å
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