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Yorodumi- PDB-5nyy: Formylglycine generating enzyme from T. curvata in complex with Cd(II) -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nyy | ||||||
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Title | Formylglycine generating enzyme from T. curvata in complex with Cd(II) | ||||||
Components | Non-specific serine/threonine protein kinaseSerine/threonine-specific protein kinase | ||||||
Keywords | TRANSFERASE / formylglycine generating enzyme / sulfatase modification / metal-binding / cadmium complex / copper enzyme | ||||||
Function / homology | Function and homology information formylglycine-generating enzyme / formylglycine-generating oxidase activity / protein oxidation / cuprous ion binding / post-translational protein modification Similarity search - Function | ||||||
Biological species | Thermomonospora curvata DSM 43183 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.28 Å | ||||||
Authors | Meury, M. / Knop, M. / Seebeck, F.P. | ||||||
Funding support | 1items
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Citation | Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017 Title: Structural Basis for Copper-Oxygen Mediated C-H Bond Activation by the Formylglycine-Generating Enzyme. Authors: Meury, M. / Knop, M. / 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 | 5nyy.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nyy.ent.gz | 103 KB | Display | PDB format |
PDBx/mmJSON format | 5nyy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/5nyy ftp://data.pdbj.org/pub/pdb/validation_reports/ny/5nyy | HTTPS FTP |
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-Related structure data
Related structure data | 5nxlSC 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 , 1 types, 1 molecules A
#1: Protein | Mass: 33082.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: In the crystal structure, the his-tag and loop region from V90 to V102 (original uniprot numbering) is disordered. Thus these residues were not modeled. Source: (gene. exp.) Thermomonospora curvata DSM 43183 (bacteria) Gene: Tcur_4811 / Production host: Escherichia coli (E. coli) References: UniProt: D1A7C3, non-specific serine/threonine protein kinase |
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-Non-polymers , 6 types, 378 molecules
#2: Chemical | ChemComp-CD / | ||||||
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#3: Chemical | ChemComp-MPD / ( | ||||||
#4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Chemical | #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: 2.25 Å3/Da / Density % sol: 45.36 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: MPD, sodium acetate, calcium chloride / PH range: 5.2 - 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 18, 2017 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.28→50.01 Å / Num. obs: 71599 / % possible obs: 98.1 % / Redundancy: 12.8 % / Biso Wilson estimate: 10.76 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.019 / Rrim(I) all: 0.067 / Net I/σ(I): 25 / Num. measured all: 919799 / Scaling rejects: 0 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NXL Resolution: 1.28→40.214 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 91.43 Å2 / Biso mean: 15.3218 Å2 / Biso min: 6.17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.28→40.214 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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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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