3MZ2

Crystal structure of a Glycerophosphoryl diester phosphodiesterase (BDI_3922) from Parabacteroides distasonis ATCC 8503 at 1.55 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glycerophosphoryl diester phosphodiesteraseA, B292Parabacteroides distasonis ATCC 8503Mutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
T [auth B]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , J [auth A] , K [auth A] , U [auth B] , V [auth B] , W [auth B] , X [auth B] , 
H [auth A],  I [auth A],  J [auth A],  K [auth A],  U [auth B],  V [auth B],  W [auth B],  X [auth B],  Y [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A] , D [auth A] , E [auth A] , F [auth A] , G [auth A] , M [auth B] , N [auth B] , O [auth B] , 
C [auth A],  D [auth A],  E [auth A],  F [auth A],  G [auth A],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
L [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.577α = 90
b = 90.481β = 111.95
c = 60.373γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXphasing
SOLVEphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Advisory, Refinement description
  • Version 1.3: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description