Crystal structure of Putative glycerophosphoryl diester phosphodiesterase (17743486) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.80 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 | 250 | Agrobacterium fabrum str. C58 | Mutation(s): 0  Gene Names: 17743486, AGR_pAT_81, Atu5061, glpQ | ||
UniProt | |||||
Find proteins for A9CLR1 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CLR1  Go to UniProtKB:  A9CLR1 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A9CLR1 | ||||
Sequence AnnotationsExpand | |||||
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Ligands 5 Unique | |||||
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ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PEG Query on PEG | J [auth A], U [auth D] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
ACT Query on ACT | H [auth A] I [auth A] M [auth B] N [auth B] Q [auth C] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CL Query on CL | G [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
MG Query on MG | F [auth A], L [auth B], P [auth C], S [auth D] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
UNL Query on UNL | E [auth A], K [auth B], O [auth C], R [auth D] | Unknown ligand JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Modified Residues 1 Unique | |||||
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ID | Chains | Type | Formula | 2D Diagram | Parent |
MSE Query on MSE | A, B, C, D | L-PEPTIDE LINKING | C5 H11 N O2 Se | MET |
Length ( Å ) | Angle ( ˚ ) |
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a = 83.427 | α = 90 |
b = 99.797 | β = 90 |
c = 134.656 | γ = 90 |
Software Name | Purpose |
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REFMAC | refinement |
PHENIX | refinement |
SOLVE | phasing |
MolProbity | model building |
SCALA | data scaling |
PDB_EXTRACT | data extraction |
MOSFLM | data reduction |