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Yorodumi- PDB-6b1v: Crystal structure of Ps i-CgsB C78S in complex with i-neocarratetraose -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b1v | |||||||||
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Title | Crystal structure of Ps i-CgsB C78S in complex with i-neocarratetraose | |||||||||
Components | Iota-carrageenan sulfatase | |||||||||
Keywords | HYDROLASE / S1 sulfatase | |||||||||
Function / homology | sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / Sulfatase Function and homology information | |||||||||
Biological species | Pseudoalteromonas (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.84 Å | |||||||||
Authors | Hettle, A.G. / Boraston, A.B. | |||||||||
Citation | Journal: Structure / Year: 2018 Title: The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme. Authors: Hettle, A.G. / Vickers, C. / Robb, C.S. / Liu, F. / Withers, S.G. / Hehemann, J.H. / 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 | 6b1v.cif.gz | 280 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b1v.ent.gz | 226.3 KB | Display | PDB format |
PDBx/mmJSON format | 6b1v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b1/6b1v ftp://data.pdbj.org/pub/pdb/validation_reports/b1/6b1v | HTTPS FTP |
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-Related structure data
Related structure data | 6b0jSC 6b0kC 6biaC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: THR / End label comp-ID: THR / Refine code: _ / Auth seq-ID: 28 - 479 / Label seq-ID: 1 - 452
NCS ensembles :
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-Components
#1: Protein | Mass: 51338.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas (bacteria) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KPH1*PLUS #2: Polysaccharide | 3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6- ...3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose-(1-4)-3,6-anhydro-2-O-sulfo-alpha-D-galactopyranose-(1-3)-4-O-sulfo-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 3.17 Å3/Da / Density % sol: 61.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 3.65 / Details: PEG 3350, citric acid, arginine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→113.4 Å / Num. obs: 47557 |
Reflection shell | Resolution: 2.84→2.89 Å / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4247 / CC1/2: 0.872 / Rpim(I) all: 0.071 / % possible all: 99.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6B0J Resolution: 2.84→113.43 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.901 / SU B: 14.047 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 104.2 Å2 / Biso mean: 46.403 Å2 / Biso min: 4.38 Å2
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Refinement step | Cycle: final / Resolution: 2.84→113.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.838→2.911 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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