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Yorodumi- PDB-6b0k: Crystal structure of Ps i-CgsB C78S in complex with k-carrapentaose -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b0k | ||||||
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Title | Crystal structure of Ps i-CgsB C78S in complex with k-carrapentaose | ||||||
Components | Iota-carrageenan sulfatase | ||||||
Keywords | HYDROLASE / S1 sulfatase | ||||||
Function / homology | sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / 3,6-anhydro-D-galactose / ARGININE / CITRIC ACID / 4-O-sulfo-beta-D-galactopyranose / Sulfatase Function and homology information | ||||||
Biological species | Pseudoalteromonas (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å | ||||||
Authors | Hettle, A. / 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 | 6b0k.cif.gz | 284.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b0k.ent.gz | 229.2 KB | Display | PDB format |
PDBx/mmJSON format | 6b0k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6b0k_validation.pdf.gz | 3.3 MB | Display | wwPDB validaton report |
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Full document | 6b0k_full_validation.pdf.gz | 3.3 MB | Display | |
Data in XML | 6b0k_validation.xml.gz | 51.6 KB | Display | |
Data in CIF | 6b0k_validation.cif.gz | 71.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0k ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0k | HTTPS FTP |
-Related structure data
Related structure data | 6b0jSC 6b1vC 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 - 478 / Label seq-ID: 1 - 451
NCS ensembles :
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-Components
-Protein / Sugars , 2 types, 11 molecules ABC
#1: Protein | Mass: 51237.699 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 #4: Sugar | ChemComp-G4S / |
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-Non-polymers , 7 types, 377 molecules
#2: Chemical | #3: Chemical | ChemComp-9RN / #5: Chemical | ChemComp-CIT / | #6: Chemical | ChemComp-ARG / | #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-CL / | #9: 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: 3.22 Å3/Da / Density % sol: 61.86 % |
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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: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 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: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→114.4 Å / Num. obs: 106480 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 15.3 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 5335 / CC1/2: 0.878 / Rpim(I) all: 0.434 / % possible all: 99.1 |
-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: 2.15→114.4 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.854 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.201 / 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: 106.18 Å2 / Biso mean: 32.308 Å2 / Biso min: 5.3 Å2
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Refinement step | Cycle: final / Resolution: 2.15→114.4 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: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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