+Open data
-Basic information
Entry | Database: PDB / ID: 4p07 | ||||||
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Title | Bacterial aryl sulfotransferase (ASST) soaked with human urine | ||||||
Components | Arylsulfate sulfotransferase AssT | ||||||
Keywords | TRANSFERASE / sulfotransferase / beta propeller / active site mutant | ||||||
Function / homology | Function and homology information aryl-sulfate sulfotransferase / arylsulfate sulfotransferase activity / aryl sulfotransferase activity / periplasmic space Similarity search - Function | ||||||
Biological species | Escherichia coli CFT073 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å | ||||||
Authors | Malojcic, G. / Owen, R.L. / Glockshuber, R. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Structural and mechanistic insights into the PAPS-independent sulfotransfer catalyzed by bacterial aryl sulfotransferase and the role of the DsbL/Dsbl system in its folding. Authors: Malojcic, G. / Owen, R.L. / Glockshuber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p07.cif.gz | 235 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p07.ent.gz | 189.4 KB | Display | PDB format |
PDBx/mmJSON format | 4p07.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p07_validation.pdf.gz | 439.1 KB | Display | wwPDB validaton report |
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Full document | 4p07_full_validation.pdf.gz | 447.9 KB | Display | |
Data in XML | 4p07_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 4p07_validation.cif.gz | 58.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/4p07 ftp://data.pdbj.org/pub/pdb/validation_reports/p0/4p07 | HTTPS FTP |
-Related structure data
Related structure data | 4p04C 4p05C 4p06C 3elqS 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 oper:
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Details | Gel filtration confirms the dimerization of the protein in solution |
-Components
#1: Protein | Mass: 63846.641 Da / Num. of mol.: 2 / Mutation: H463N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Gene: assT, LF82_506 / Production host: Escherichia coli (E. coli) References: UniProt: E2QE64, UniProt: A0A0D6H805*PLUS, aryl-sulfate sulfotransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.82 Å3/Da / Density % sol: 67.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Sitting drop vapor diffusion method by equilibrating 1.5 ?l of protein solution (22 mg/ml, in 20 mM 4-morpholinepropanesulfonic acid/NaOH pH 7.5, 100 mM NaCl) with 0.5 ?l of reservoir ...Details: Sitting drop vapor diffusion method by equilibrating 1.5 ?l of protein solution (22 mg/ml, in 20 mM 4-morpholinepropanesulfonic acid/NaOH pH 7.5, 100 mM NaCl) with 0.5 ?l of reservoir solution consisting of 1.8 M Li2SO4 and 100 mM cacodylic acid/NaOH pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 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: 2.59→48.4 Å / Num. obs: 58584 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.13 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.59→2.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 1.035 / Mean I/σ(I) obs: 1.7 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELQ Resolution: 2.59→48.4 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.447 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.67 Å2
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Refinement step | Cycle: 1 / Resolution: 2.59→48.4 Å
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Refine LS restraints |
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