+Open data
-Basic information
Entry | Database: PDB / ID: 4upi | |||||||||
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Title | Dimeric sulfatase SpAS1 from Silicibacter pomeroyi | |||||||||
Components | SULFATASE FAMILY PROTEIN | |||||||||
Keywords | HYDROLASE / SUPERFAMILY / ALKALINE PHOSPHATASE SUPERFAMILY | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | RUEGERIA POMEROYI (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | |||||||||
Authors | Jonas, S. / van Loo, B. / Hollfelder, F. / Hyvonen, M. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2019 Title: Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily. Authors: van Loo, B. / Bayer, C.D. / Fischer, G. / Jonas, S. / Valkov, E. / Mohamed, M.F. / Vorobieva, A. / Dutruel, C. / Hyvonen, M. / Hollfelder, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4upi.cif.gz | 249.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upi.ent.gz | 199.2 KB | Display | PDB format |
PDBx/mmJSON format | 4upi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upi ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upi | HTTPS FTP |
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-Related structure data
Related structure data | 4uphC 4upkC 4uplC 1e2sS 1fsuS 1hthS 1p49S 2vqrS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 65376.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: FORMYL GLYCINE IN POSITION 77, MODIFIED FROM CYSTEINE, WITH PARTIAL MODIFICATION Source: (gene. exp.) RUEGERIA POMEROYI (bacteria) / Strain: DSS-3 Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES (DSMZ) Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LLA5 |
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#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.51 % / Description: NONE |
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Crystal grow | Details: 0.1 M TRIS-HCL PH 8.0, 20% (W/V) PEG 6000, 0.75 M LICL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→74.99 Å / Num. obs: 160317 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 23.378 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.97 |
Reflection shell | Resolution: 1.25→1.28 Å / Redundancy: 2.87 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.2 / % possible all: 89.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1E2S, 2VQR, 1FSU, 1P49, 1HTH AS AN ENSEMBLE Resolution: 1.25→37.497 Å / SU ML: 0.1 / σ(F): 1.36 / Phase error: 17.41 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.02 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→37.497 Å
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Refine LS restraints |
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LS refinement shell |
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