Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution
Joint Center for Structural Genomics (JCSG)To be published.
Experimental Data Snapshot
wwPDB Validation   3D Report Full Report
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Glycerophosphoryl diester phosphodiesterase | 292 | Parabacteroides distasonis ATCC 8503 | Mutation(s): 0  Gene Names: BDI_3922 | ||
UniProt | |||||
Find proteins for A6LIT8 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LIT8  Go to UniProtKB:  A6LIT8 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A6LIT8 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 4 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PE4 Query on PE4 | T [auth B] | 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N | |||
PG4 Query on PG4 | H [auth A] I [auth A] J [auth A] K [auth A] U [auth B] | TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N | |||
SO4 Query on SO4 | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
NA Query on NA | L [auth B] | SODIUM ION Na FKNQFGJONOIPTF-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 ( ˚ ) |
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a = 53.577 | α = 90 |
b = 90.481 | β = 111.95 |
c = 60.373 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
PHENIX | refinement |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |
PHENIX | phasing |
SOLVE | phasing |