+Open data
-Basic information
Entry | Database: PDB / ID: 2q17 | ||||||
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Title | Formylglycine Generating Enzyme from Streptomyces coelicolor | ||||||
Components | formylglycine generating enzyme | ||||||
Keywords | UNKNOWN FUNCTION / FGE / formylglycine / sulfatase | ||||||
Function / homology | Function and homology information formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / cupric ion binding / post-translational protein modification / calcium ion binding Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Carlson, B.L. / Ballister, E.R. / Skordalakes, E. / King, D.S. / Breidenbach, M.A. / Gilmore, S.A. / Berger, J.M. / Bertozzi, C.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Function and structure of a prokaryotic formylglycine-generating enzyme. Authors: Carlson, B.L. / Ballister, E.R. / Skordalakes, E. / King, D.S. / Breidenbach, M.A. / Gilmore, S.A. / Berger, J.M. / Bertozzi, C.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q17.cif.gz | 534.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q17.ent.gz | 432.5 KB | Display | PDB format |
PDBx/mmJSON format | 2q17.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2q17_validation.pdf.gz | 483.6 KB | Display | wwPDB validaton report |
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Full document | 2q17_full_validation.pdf.gz | 495.6 KB | Display | |
Data in XML | 2q17_validation.xml.gz | 59.6 KB | Display | |
Data in CIF | 2q17_validation.cif.gz | 86.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/2q17 ftp://data.pdbj.org/pub/pdb/validation_reports/q1/2q17 | HTTPS FTP |
-Related structure data
Related structure data | 1y1eS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 37482.152 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9F3C7 #2: Chemical | ChemComp-CA / #3: 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: 3.39 Å3/Da / Density % sol: 63.71 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8 Details: 100 mM Tris, 2.4 M ammonium formate, 0.3% -octylglucoside, 3.2% 2-butanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 123276 |
Reflection shell | Resolution: 2.1→2.17 Å |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y1E Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 12.851 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.563 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.231 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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