+Open data
-Basic information
Entry | Database: PDB / ID: 4upl | ||||||
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Title | Dimeric sulfatase SpAS2 from Silicibacter pomeroyi | ||||||
Components | SULFATASE FAMILY PROTEIN | ||||||
Keywords | HYDROLASE / ALKALINE PHOSPHATASE SUPERFAMILY | ||||||
Function / homology | Function and homology information | ||||||
Biological species | RUEGERIA POMEROYI (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.805 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 | 4upl.cif.gz | 249.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4upl.ent.gz | 198.9 KB | Display | PDB format |
PDBx/mmJSON format | 4upl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4upl_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 4upl_full_validation.pdf.gz | 440.8 KB | Display | |
Data in XML | 4upl_validation.xml.gz | 47.9 KB | Display | |
Data in CIF | 4upl_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/up/4upl ftp://data.pdbj.org/pub/pdb/validation_reports/up/4upl | HTTPS FTP |
-Related structure data
Related structure data | 4uphC 4upiSC 4upkC 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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Unit cell |
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-Components
#1: Protein | Mass: 64660.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RUEGERIA POMEROYI (bacteria) / Strain: DSS-3 Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURE (DSMZ) Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LMH0 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | SEQUENCE CONTAINS N-TERMINAL STREPTAG | |
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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: 2.28 Å3/Da / Density % sol: 46.02 % / Description: NONE |
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Crystal grow | Details: 20% PEG3350, 0.2 M AMMONIUM FORMATE |
-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 QUANTUM 315r / Detector: CCD / Date: Oct 5, 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: 1.8→48.89 Å / Num. obs: 108165 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.39 |
Reflection shell | Resolution: 1.8→1.91 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.83 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4UPI Resolution: 1.805→47.459 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 20.23 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.805→47.459 Å
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Refine LS restraints |
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LS refinement shell |
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