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- PDB-3ett: Crystal structure of a bacterial arylsulfate sulfotransferase cat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ett | ||||||
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Title | Crystal structure of a bacterial arylsulfate sulfotransferase catalytic intermediate with 4-nitrophenol bound in the active site | ||||||
![]() | Arylsulfate sulfotransferase | ||||||
![]() | TRANSFERASE / beta propeller / sulfohistidine / protein-substrate complex / periplasm / transesterification / sulfate / phenol / bacteria / transferase 4-nitrophenol / p-nitrophenol / p-nitrophenylsulfate | ||||||
Function / homology | ![]() aryl-sulfate sulfotransferase / arylsulfate sulfotransferase activity / aryl sulfotransferase activity / periplasmic space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Glockshuber, R. | ||||||
![]() | ![]() Title: A structural and biochemical basis for PAPS-independent sulfuryl transfer by aryl sulfotransferase from uropathogenic Escherichia coli. Authors: Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Brozzo, M.S. / Dreher-Teo, H. / Glockshuber, R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 247.3 KB | Display | ![]() |
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PDB format | ![]() | 198.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 468.7 KB | Display | ![]() |
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Full document | ![]() | 475.5 KB | Display | |
Data in XML | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 71.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3elqSC ![]() 3etsC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 571 / Label seq-ID: 1 - 571
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Components
#1: Protein | Mass: 63926.703 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: B3HTA9, UniProt: Q8FDI4*PLUS, aryl-sulfate sulfotransferase #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 1.8M lithium sulfate, 0.1M sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2008 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 108768 / Num. obs: 108768 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.994 / Redundancy: 3.8 % / Biso Wilson estimate: 30.47 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.08 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.46 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ELQ Resolution: 2.1→33.98 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.709 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.151 / ESU R Free: 0.149 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. PHENIX WAS ALSO USED FOR REFINEMENT.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→33.98 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7510 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.1→2.16 Å / Total num. of bins used: 20
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