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Yorodumi- PDB-3ets: Crystal structure of a bacterial arylsulfate sulfotransferase cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ets | ||||||
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Title | Crystal structure of a bacterial arylsulfate sulfotransferase catalytic intermediate with 4-methylumbelliferone bound in the active site | ||||||
Components | Arylsulfate sulfotransferase | ||||||
Keywords | TRANSFERASE / beta propeller / sulfohistidine / protein-substrate complex / periplasm / transesterification / sulfate / phenol / bacteria / transferase 4-methylumbelliferone / 4-methylumbelliferylsulfate | ||||||
Function / homology | Function and homology information aryl-sulfate sulfotransferase / arylsulfate sulfotransferase activity / aryl sulfotransferase activity / periplasmic space / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Malojcic, G. / Owen, R.L. / Grimshaw, J.P. / Glockshuber, R. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2008 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ets.cif.gz | 234.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ets.ent.gz | 188.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ets.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ets_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 3ets_full_validation.pdf.gz | 476.6 KB | Display | |
Data in XML | 3ets_validation.xml.gz | 41.6 KB | Display | |
Data in CIF | 3ets_validation.cif.gz | 58.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/et/3ets ftp://data.pdbj.org/pub/pdb/validation_reports/et/3ets | HTTPS FTP |
-Related structure data
Related structure data | 3elqSC 3ettC 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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2 |
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Unit cell |
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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.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: ASTA, EcF11_2091 / Plasmid: PDSBA3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 15, 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: 2.4→48 Å / Num. all: 102818 / Num. obs: 102818 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.994 / Redundancy: 7.6 % / Biso Wilson estimate: 51.21 Å2 / Rmerge(I) obs: 0.143 / Rsym value: 0.134 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.51 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELQ Resolution: 2.4→38.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.353 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.213 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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: 41.17 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→38.43 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: 2.4→2.46 Å / Total num. of bins used: 20
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