3NO3

Crystal structure of a glycerophosphodiester phosphodiesterase (BDI_0402) from Parabacteroides distasonis ATCC 8503 at 1.89 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3NO3/pdb

• Classification: HYDROLASE
• Organism(s): Parabacteroides distasonis ATCC 8503
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-24 Released: 2010-07-28 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.177 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 

Literature

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.08 kDa 
• Atom Count: 2,291 
• Modelled Residue Count: 238 
• Deposited Residue Count: 238 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glycerophosphodiester phosphodiesterase	A	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	E [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.89 Å
• R-Value Free: 0.177 
• R-Value Work: 0.150 
• R-Value Observed: 0.151 
• Space Group: C 1 2 1
• Diffraction Data: https://doi.org/10.18430/M33NO3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.46	α = 90
b = 40.876	β = 99.39
c = 48.328	γ = 90

Software Package:

Software Name	Purpose
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-28 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-07-28
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-02-01
  Changes: Database references, Derived calculations