4DU5 | pdb_00004du5

Crystal structure of PfkB protein from Polaromonas sp. JS666

• PDB DOI: https://doi.org/10.2210/pdb4DU5/pdb

• Classification: TRANSFERASE
• Organism(s): Polaromonas sp. JS666
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-21 Released: 2012-03-21 
• Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hellerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.296 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of PfkB protein from Polaromonas sp. JS666

Agarwal, R., Almo, S.C., Swaminathan, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 144.22 kDa 
• Atom Count: 8,654 
• Modeled Residue Count: 1,177 
• Deposited Residue Count: 1,344 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PfkB	A, B, C, D	336	Polaromonas sp. JS666	Mutation(s): 0  Gene Names: Bpro_1737

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.296 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.923	α = 90
b = 83.084	β = 90
c = 196.202	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
MOLREP	phasing
Coot	model building
ARP	model building
AutoSol	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Agarwal, R., Chamala, S., Evans, B., Foti, R., Gizzi, A., Hellerich, B., Kar, A., Lafleur, J., Siedel, R., Villigas, G., Zencheck, W., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2023-12-06
  Changes: Data collection
• Version 1.4: 2024-10-16
  Changes: Structure summary