A structural study of TatD from Staphylococcus aureus elucidates a putative DNA-binding mode of a Mg2+-dependent nuclease.
Lee, K.-Y., Cheon, S.-H., Kim, D.-G., Lee, S.J., Lee, B.-J.(2020) IUCrJ 7: 509-521
Experimental Data Snapshot
(2020) IUCrJ 7: 509-521
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Deoxyribonuclease YcfH | 273 | Staphylococcus aureus | Mutation(s): 0  Gene Names:  yabD, tatP, ycfH, ycfH_1, BN1321_120011, C7P97_09010, CSC83_12190, CSC87_02770, EP54_03105, EQ90_10980... EC: 3.1.21 | ||
UniProt | |||||
Find proteins for W8U6D8 (Staphylococcus aureus) Explore W8U6D8  Go to UniProtKB:  W8U6D8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | W8U6D8 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 2 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PO4 (Subject of Investigation/LOI) Query on PO4 | E [auth A], F [auth A], I [auth B], J [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
NI (Subject of Investigation/LOI) Query on NI | C [auth A], D [auth A], G [auth B], H [auth B] | NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 47.627 | α = 90 |
b = 77.832 | β = 98.81 |
c = 77.378 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
PHENIX | phasing |
Funding Organization | Location | Grant Number |
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National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2018R1A2A1A19018526 |
National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2018R1A5A2024425 |
National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2016R1C1B2014609 |
National Research Foundation (NRF, Korea) | Korea, Republic Of | NRF-2019R1H1A1102102 |