Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
Experimental Data Snapshot
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Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
glycerophosphodiester phosphodiesterase | 238 | Parabacteroides distasonis ATCC 8503 | Mutation(s): 0  Gene Names: BDI_0402 | ||
UniProt | |||||
Find proteins for A6L916 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6L916  Go to UniProtKB:  A6L916 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A6L916 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 3 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PEG Query on PEG | E [auth A] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
GOL Query on GOL | D [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
MG Query on MG | B [auth A], C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 137.46 | α = 90 |
b = 40.876 | β = 99.39 |
c = 48.328 | γ = 90 |
Software Name | Purpose |
---|---|
SHELX | phasing |
REFMAC | refinement |
XSCALE | data scaling |
PDB_EXTRACT | data extraction |
XDS | data reduction |
SHELXD | phasing |
autoSHARP | phasing |