4PY9 | pdb_00004py9

Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192

• PDB DOI: https://doi.org/10.2210/pdb4PY9/pdb
• Entry: 4PY9 supersedes: 3DMA

• Classification: UNKNOWN FUNCTION
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-26 Released: 2014-06-25 
• Deposition Author(s): Seetharaman, J., Abashidze, M., Wang, H., Janjua, H., Foote, E.L., Xiao, R., Nair, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.264 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

Crystal structure of an exopolyphosphatase-related protein from Bacteroides Fragilis. Northeast Structural Genomics target BFR192

Seetharaman, J., Abashidze, M., Wang, H., Janjua, H., Foote, E.L., Xiao, R., Nair, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.24 kDa 
• Atom Count: 2,858 
• Modeled Residue Count: 340 
• Deposited Residue Count: 343 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative exopolyphosphatase-related protein	A	343	Bacteroides fragilis	Mutation(s): 0  Gene Names: BF3900
UniProt
Find proteins for Q64PD9 (Bacteroides fragilis (strain YCH46)) Explore Q64PD9  Go to UniProtKB:  Q64PD9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	B [auth A], C [auth A], D [auth A], E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NA	F [auth A], G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.25 Å
• R-Value Free:  0.264 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.892	α = 90
b = 90.892	β = 90
c = 107.684	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Seetharaman, J., Abashidze, M., Wang, H., Janjua, H., Foote, E.L., Xiao, R., Nair, R., Everett, J.K., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)
• This entry supersedes: 3DMA

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary