[English] 日本語
Yorodumi- PDB-6pt6: Crystal structure of PsS1_NC C84S in complex with i-neocarratetraose -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pt6 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of PsS1_NC C84S in complex with i-neocarratetraose | |||||||||
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 / Sulfatase Function and homology information | |||||||||
Biological species | Pseudoalteromonas fuliginea (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å | |||||||||
Authors | Hettle, A.G. / Boraston, A.B. | |||||||||
Funding support | Canada, 1items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6pt6.cif.gz | 208 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6pt6.ent.gz | 161.6 KB | Display | PDB format |
PDBx/mmJSON format | 6pt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pt6_validation.pdf.gz | 388.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6pt6_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | 6pt6_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6pt6_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/6pt6 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/6pt6 | HTTPS FTP |
-Related structure data
Related structure data | 6pnuC 6popC 6prmC 6psmC 6psoC 6pt4SC 6pt9C 6ptkC 6ptmC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
-Components
#1: Protein | Mass: 56678.719 Da / Num. of mol.: 2 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 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.59 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Hepes, sodium acetate trihydrate, arginine, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å |
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54187 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 46858 / % possible obs: 95.3 % / Redundancy: 4 % / CC1/2: 0.994 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.25→2.29 Å / Rmerge(I) obs: 0.292 / Num. unique obs: 4243 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6PT4 Resolution: 2.25→31.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 7.017 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 84.47 Å2 / Biso mean: 30.727 Å2 / Biso min: 17.1 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.25→31.78 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 16190 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.251→2.309 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|