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Yorodumi- PDB-6xtr: Crystal structure reveals non-coordinative binding of O2 to the c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xtr | |||||||||
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Title | Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Cu:S:O2-1c complex | |||||||||
Components |
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Keywords | TRANSFERASE / Formylglycine-generating enzyme / complex / substrate analog / copper | |||||||||
Function / homology | Function and homology information N-acetylglucosamine-6-sulfatase activity / formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / glycosaminoglycan binding / cuprous ion binding / post-translational protein modification / metal ion binding Similarity search - Function | |||||||||
Biological species | Thermomonospora curvata (bacteria) Thermomonospora curvata DSM 43183 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | |||||||||
Authors | Leisinger, F. / Seebeck, F.P. | |||||||||
Funding support | Switzerland, European Union, 2items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2020 Title: Non-Coordinative Binding of O2 at the Active Center of a Copper-Dependent Enzyme Authors: Leisinger, F. / Miarzlou, D.A. / Seebeck, F.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xtr.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xtr.ent.gz | 62.9 KB | Display | PDB format |
PDBx/mmJSON format | 6xtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xtr_validation.pdf.gz | 335 KB | Display | wwPDB validaton report |
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Full document | 6xtr_full_validation.pdf.gz | 335.7 KB | Display | |
Data in XML | 6xtr_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 6xtr_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xtr ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xtr | HTTPS FTP |
-Related structure data
Related structure data | 6xtlC 6xtmC 6xtnC 6xtoC 6xtpC 6xtqC 6xtsC 6s07S 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
-Protein / Protein/peptide , 2 types, 2 molecules AC
#1: Protein | Mass: 33336.852 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomonospora curvata (strain ATCC 19995 / DSM 43183 / JCM 3096 / NBRC 15933 / NCIMB 10081 / Henssen B9) (bacteria) Gene: Tcur_4811 / Plasmid: pET19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS References: UniProt: D1A7C3, formylglycine-generating enzyme |
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#2: Protein/peptide | Mass: 1531.755 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: modified sulfatase sequence motif Source: (synth.) Thermomonospora curvata DSM 43183 (bacteria) References: UniProt: D1ADF2*PLUS |
-Non-polymers , 6 types, 347 molecules
#3: Chemical | ChemComp-CU1 / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-OXY / | #7: Chemical | ChemComp-SOA / | #8: 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: 2.28 Å3/Da / Density % sol: 45.98 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 7-12 % PEG 8000, 0.2-0.3 M MgCl2, Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0006777109999 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 5, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0006777109999 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→46.19 Å / Num. obs: 100095 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 13.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.014 / Rrim(I) all: 0.049 / Net I/σ(I): 25.3 / Num. measured all: 1277049 / Scaling rejects: 31 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S07 Resolution: 1.2→46.189 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.11
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.89 Å2 / Biso mean: 17.7215 Å2 / Biso min: 8.83 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.2→46.189 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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