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Yorodumi- PDB-6xto: Crystal structure reveals non-coordinative binding of O2 to the c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xto | |||||||||
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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:NO 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: 1.4 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 | 6xto.cif.gz | 88.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xto.ent.gz | 63.3 KB | Display | PDB format |
PDBx/mmJSON format | 6xto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xto_validation.pdf.gz | 331.4 KB | Display | wwPDB validaton report |
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Full document | 6xto_full_validation.pdf.gz | 332.2 KB | Display | |
Data in XML | 6xto_validation.xml.gz | 17.7 KB | Display | |
Data in CIF | 6xto_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xt/6xto ftp://data.pdbj.org/pub/pdb/validation_reports/xt/6xto | HTTPS FTP |
-Related structure data
Related structure data | 6xtlC 6xtmC 6xtnC 6xtpC 6xtqC 6xtrC 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: 1387.625 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 , 5 types, 373 molecules
#3: Chemical | ChemComp-CU1 / | ||||||
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#4: Chemical | #5: Chemical | ChemComp-NO / | #6: Chemical | ChemComp-SOA / | #7: 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: 2.31 Å3/Da / Density % sol: 46.65 % / Mosaicity: 0.28 ° |
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Crystal grow | Temperature: 303.15 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: 1.3→46.32 Å / Num. obs: 79498 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.032 / Rrim(I) all: 0.103 / Net I/σ(I): 14.9 / Num. measured all: 854872 / Scaling rejects: 5081 | ||||||||||||||||||||||||||||||
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: 1.4→38.944 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.83 Å2 / Biso mean: 15.6975 Å2 / Biso min: 5.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→38.944 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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