+Open data
-Basic information
Entry | Database: PDB / ID: 6k20 | ||||||
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Title | Structure of Apo YdiU | ||||||
Components | Protein adenylyltransferase SelO | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Protein adenylyltransferase SelO / Protein adenylyltransferase SelO / AMPylase activity / protein adenylyltransferase / protein adenylylation / magnesium ion binding / ATP binding / Protein adenylyltransferase SelO / Protein adenylyltransferase SelO Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å | ||||||
Authors | Li, B. / Yang, Y. / Ma, Y. | ||||||
Citation | Journal: To Be Published Title: Structure of Apo-YdiU Authors: Li, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k20.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k20.ent.gz | 82 KB | Display | PDB format |
PDBx/mmJSON format | 6k20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k20_validation.pdf.gz | 424.7 KB | Display | wwPDB validaton report |
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Full document | 6k20_full_validation.pdf.gz | 428.4 KB | Display | |
Data in XML | 6k20_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6k20_validation.cif.gz | 27.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/6k20 ftp://data.pdbj.org/pub/pdb/validation_reports/k2/6k20 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 54480.004 Da / Num. of mol.: 1 / Mutation: C272S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ydiU Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A024L327, UniProt: P77649*PLUS, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases |
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#2: Chemical | ChemComp-MG / |
#3: 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: 3.38 Å3/Da / Density % sol: 63.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: 10% peg200, 0.1M Bistris pH9.0, 18%PEG 8,000 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 31, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.58→29.34 Å / Num. obs: 22642 / % possible obs: 93.6 % / Redundancy: 1 % / Net I/σ(I): 20.5 |
Reflection shell | Resolution: 2.58→2.69 Å / Num. unique obs: 2275 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→27.891 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.63
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.58→27.891 Å
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Refine LS restraints |
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LS refinement shell |
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