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Open data
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Basic information
Entry | Database: PDB / ID: 7stv | ||||||
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Title | Crystal structure of sulfatase from Pedobacter yulinensis | ||||||
![]() | N-acetylgalactosamine-6-sulfatase | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | O'Malley, A. / Schlachter, C.R. / Grimes, L.L. / Tomashek, J.J. / Lee, A.L. / Chruszcz, M. | ||||||
Funding support | 1items
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 179.3 KB | Display | ![]() |
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PDB format | ![]() | 135.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 852.2 KB | Display | ![]() |
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Full document | ![]() | 857.8 KB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sttSC ![]() 7stuC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 122 molecules ![](data/chem/img/CIT.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |