+Open data
-Basic information
Entry | Database: PDB / ID: 7stt | ||||||
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Title | Crystal structure of sulfatase from Pedobacter yulinensis | ||||||
Components | N-acetylgalactosamine-6-sulfatase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / sulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / MALONATE ION / N-acetylgalactosamine-6-sulfatase Function and homology information | ||||||
Biological species | Pedobacter yulinensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å | ||||||
Authors | O'Malley, A. / Schlachter, C.R. / Grimes, L.L. / Tomashek, J.J. / Lee, A.L. / Chruszcz, M. | ||||||
Funding support | 1items
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Citation | Journal: Molecules / Year: 2021 Title: Purification, Characterization, and Structural Studies of a Sulfatase from Pedobacter yulinensis . Authors: Schlachter, C.R. / O'Malley, A. / Grimes, L.L. / Tomashek, J.J. / Chruszcz, M. / Lee, L.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7stt.cif.gz | 189.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7stt.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 7stt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/7stt ftp://data.pdbj.org/pub/pdb/validation_reports/st/7stt | HTTPS FTP |
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-Related structure data
Related structure data | 7stuC 7stvC 6ustS 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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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 51392.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pedobacter yulinensis (bacteria) / Gene: C7T94_09545 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2T3HKC0 |
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-Non-polymers , 5 types, 561 molecules
#2: Chemical | ChemComp-MLI / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CA / | #6: Water | ChemComp-HOH / | |
-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: 2.28 Å3/Da / Density % sol: 46.03 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40 Å / Num. obs: 59449 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.024 / Rrim(I) all: 0.079 / Rsym value: 0.068 / Net I/σ(I): 35.25 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2 / Num. unique obs: 2069 / CC1/2: 0.859 / CC star: 0.961 / Rpim(I) all: 0.186 / Rrim(I) all: 0.487 / Rsym value: 0.449 / % possible all: 67.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6UST Resolution: 1.603→39.366 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.811 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.078 / ESU R Free: 0.079 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.603→39.366 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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