+Open data
-Basic information
Entry | Database: PDB / ID: 3elq | ||||||
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Title | Crystal structure of a bacterial arylsulfate sulfotransferase | ||||||
Components | Arylsulfate sulfotransferase | ||||||
Keywords | TRANSFERASE / BETA PROPELLER / PROTEIN-SUBSTRATE COMPLEX / PERIPLASM / TRANSESTERIFICATION / SULFATE / PHENOL / BACTERIA | ||||||
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 / SAD / Resolution: 2 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 | 3elq.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3elq.ent.gz | 206.7 KB | Display | PDB format |
PDBx/mmJSON format | 3elq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3elq_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 3elq_full_validation.pdf.gz | 444.2 KB | Display | |
Data in XML | 3elq_validation.xml.gz | 50 KB | Display | |
Data in CIF | 3elq_validation.cif.gz | 75.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/el/3elq ftp://data.pdbj.org/pub/pdb/validation_reports/el/3elq | HTTPS FTP |
-Related 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:
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-Components
#1: Protein | Mass: 63846.641 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 | ChemComp-SO4 / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 | ||||||||||||||||||
Detector |
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Radiation |
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Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 2→60 Å / Num. obs: 124546 / % possible obs: 99 % / Observed criterion σ(I): 2.994 / Redundancy: 12.1 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 20.3 | ||||||||||||||||||
Reflection shell | Resolution: 2→2.06 Å / Redundancy: 6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.5 / Num. unique all: 7897 / Rsym value: 0.4 / % possible all: 94.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→33.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.284 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.147 / ESU R Free: 0.144 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: 33.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→33.9 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 7516 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.06 Å / Total num. of bins used: 20
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