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Yorodumi- PDB-6ptk: Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ptk | ||||||
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Title | Crystal structure of the sulfatase PsS1_NC C84A with bound sulfate ion | ||||||
Components | exo-2S-iota carrageenan S1 sulfatase | ||||||
Keywords | HYDROLASE / S1 sulfatase | ||||||
Function / homology | Sulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3,6-anhydro-D-galactose / 4-O-sulfo-beta-D-galactopyranose / Sulfatase Function and homology information | ||||||
Biological species | Pseudoalteromonas fuliginea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å | ||||||
Authors | Hettle, A.G. / Boraston, A.B. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Commun Biol / Year: 2019 Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies. Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ptk.cif.gz | 429 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ptk.ent.gz | 343.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ptk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ptk_validation.pdf.gz | 3 MB | Display | wwPDB validaton report |
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Full document | 6ptk_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6ptk_validation.xml.gz | 81.6 KB | Display | |
Data in CIF | 6ptk_validation.cif.gz | 125.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/6ptk ftp://data.pdbj.org/pub/pdb/validation_reports/pt/6ptk | HTTPS FTP |
-Related structure data
Related structure data | 6pnuC 6popC 6prmC 6psmC 6psoC 6pt4SC 6pt6C 6pt9C 6ptmC S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / Refine code: _
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 56662.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Strain: PS47 / Gene: EU509_08820 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A063KNC1*PLUS #4: Sugar | ChemComp-G4S / |
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-Non-polymers , 6 types, 1884 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-9RN / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-GOL / #7: Chemical | ChemComp-CA / #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.58 Å3/Da / Density % sol: 52.41 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000, Na cacodylate, Ca acetate, LiCl2, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→68.78 Å / Num. obs: 201748 / % possible obs: 87 % / Redundancy: 4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.75→1.84 Å / Rmerge(I) obs: 0.202 / Num. unique obs: 28359 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PT4 Resolution: 1.75→56.75 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.605 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.091 Details: 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 53.81 Å2 / Biso mean: 13.625 Å2 / Biso min: 5.76 Å2
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Refinement step | Cycle: final / Resolution: 1.75→56.75 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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