3K0Y

Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3K0Y/pdb

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


• Deposited: 2009-09-25 Released: 2009-10-06 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 

Literature

Crystal structure of Putative TOXIN related protein (YP_001303978.1) from Parabacteroides distasonis ATCC 8503 at 2.16 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 and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.61 kDa 
• Atom Count: 1,670 
• Modelled Residue Count: 198 
• Deposited Residue Count: 229 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative TOXIN related protein	A	229	Parabacteroides distasonis ATCC 8503	Mutation(s): 0  Gene Names: BDI_2637
UniProt
Find proteins for A6LF92 (Parabacteroides distasonis (strain ATCC 8503 / DSM 20701 / CIP 104284 / JCM 5825 / NCTC 11152)) Explore A6LF92  Go to UniProtKB:  A6LF92

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2PE	B [auth A], C [auth A]	NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-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: 2.16 Å
• R-Value Free: 0.235 
• R-Value Work: 0.203 
• R-Value Observed: 0.205 
• Space Group: P 3₁ 2 1
• Diffraction Data: https://doi.org/10.18430/M33K0Y

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.722	α = 90
b = 71.722	β = 90
c = 102.566	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-06 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations