+Open data
-Basic information
Entry | Database: PDB / ID: 7stv | ||||||
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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 / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / hydrolase activity / CITRIC ACID / N-acetylgalactosamine-6-sulfatase Function and homology information | ||||||
Biological species | Pedobacter yulinensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 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 | 7stv.cif.gz | 179.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7stv.ent.gz | 135.4 KB | Display | PDB format |
PDBx/mmJSON format | 7stv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/7stv ftp://data.pdbj.org/pub/pdb/validation_reports/st/7stv | HTTPS FTP |
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-Related structure data
Related structure data | 7sttSC 7stuC 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, 122 molecules
#2: Chemical | ChemComp-CIT / | ||||||
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#3: Chemical | #4: Chemical | #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: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate pH 5.5, 20% w/v polyethylene glycol 3000 |
-Data collection
Diffraction | Mean temperature: 295 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: 2.34→40 Å / Num. obs: 19275 / % possible obs: 98.8 % / Redundancy: 9.2 % / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.048 / Rrim(I) all: 0.148 / Rsym value: 0.101 / Net I/σ(I): 18.5 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2 / Num. unique obs: 936 / CC1/2: 0.948 / CC star: 0.986 / Rpim(I) all: 0.175 / Rrim(I) all: 0.525 / Rsym value: 0.489 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7STT Resolution: 2.35→34.232 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.712 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.393 / ESU R Free: 0.244 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: 56.402 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→34.232 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -33.34 Å / Origin y: 6.47 Å / Origin z: -16.9122 Å
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Refinement TLS group | Selection: ALL |