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Yorodumi- PDB-6hhm: Crystal structure of the family S1_7 ulvan-specific sulfatase FA2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hhm | |||||||||
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Title | Crystal structure of the family S1_7 ulvan-specific sulfatase FA22070 from Formosa agariphila | |||||||||
Components | Arylsulfatase | |||||||||
Keywords | HYDROLASE / Formosa agariphila algal polysaccharide carrageenan sulfatase | |||||||||
Function / homology | Function and homology information iduronate-2-sulfatase activity / Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / periplasmic space / metal ion binding Similarity search - Function | |||||||||
Biological species | Formosa agariphila (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å | |||||||||
Authors | Roret, T. / Prechoux, A. / Michel, G. / Czjzek, M. | |||||||||
Funding support | France, 2items
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Citation | Journal: Nat.Chem.Biol. / Year: 2019 Title: A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan. Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, ...Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, M.D. / Trautwein-Schult, A. / Becher, D. / Schweder, T. / Bornscheuer, U.T. / Hehemann, J.H. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hhm.cif.gz | 287.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hhm.ent.gz | 232.3 KB | Display | PDB format |
PDBx/mmJSON format | 6hhm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/6hhm ftp://data.pdbj.org/pub/pdb/validation_reports/hh/6hhm | HTTPS FTP |
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-Related structure data
Related structure data | 6hhnC 6hpdC 6hr5C 5fqlS 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
#1: Protein | Mass: 53928.723 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Formosa agariphila (bacteria) / Gene: BN863_22070 / Production host: Escherichia coli (E. coli) / References: UniProt: T2KPK5, arylsulfatase (type I) |
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#2: Chemical | ChemComp-CA / |
#3: 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: 2.08 Å3/Da / Density % sol: 40.74 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM MIB pH 5.0 25 % PEG 1,500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.23→48.37 Å / Num. obs: 131006 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 1.23→1.3 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 18927 / CC1/2: 0.929 / Rpim(I) all: 0.203 / Rrim(I) all: 0.448 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5FQL Resolution: 1.23→45.239 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.23→45.239 Å
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Refine LS restraints |
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LS refinement shell |
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