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- PDB-6xtl: Crystal structure reveals non-coordinative binding of O2 to the c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xtl | |||||||||
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Title | Crystal structure reveals non-coordinative binding of O2 to the copper center of the formylglycine-generating enzyme - FGE:Ag:S complex | |||||||||
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![]() | TRANSFERASE / Formylglycine-generating enzyme / complex / substrate analog / copper | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Leisinger, F. / Seebeck, F.P. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.1 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 329.5 KB | Display | ![]() |
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Full document | ![]() | 329.6 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6xtmC ![]() 6xtnC ![]() 6xtoC ![]() 6xtpC ![]() 6xtqC ![]() 6xtrC ![]() 6xtsC ![]() 6s07S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() Gene: Tcur_4811 / Plasmid: pET19 / Production host: ![]() ![]() References: UniProt: D1A7C3, formylglycine-generating enzyme |
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#2: Protein/peptide | Mass: 1531.755 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: modified sulfatase sequence motif Source: (gene. exp.) ![]() Production host: ![]() ![]() |
-Non-polymers , 6 types, 268 molecules ![](data/chem/img/AG.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SOA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/SOA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-AG / | ||||||||
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#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-CL / | #7: Chemical | ChemComp-SOA / | #8: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.69 % |
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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: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 5, 2019 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98298 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.41 Å / Num. obs: 30598 / % possible obs: 99.9 % / Redundancy: 12.4 % / Biso Wilson estimate: 13.79 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.05 / Rrim(I) all: 0.175 / Net I/σ(I): 14 / Num. measured all: 378075 / Scaling rejects: 515 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / % possible all: 99.7
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6S07 Resolution: 1.8→46.401 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.29 Å2 / Biso mean: 14.6044 Å2 / Biso min: 5.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→46.401 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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