7BMM

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

• PDB DOI: https://doi.org/10.2210/pdb7BMM/pdb

• Classification: TRANSFERASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-01-20 Released: 2021-04-07 
• Deposition Author(s): Silva, S.T.N., Romao, C.
• Funding Organization(s): Fundacao para a Ciencia e a Tecnologia

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Literature

Crystal structure of Polyphosphate Kinase 2 from Deinococcus radiodurans in apo form

Silva, S.T.N., Romao, C.

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 Evidence: gel filtration

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: 122.95 kDa 
• Atom Count: 9,183 
• Modelled Residue Count: 1,064 
• Deposited Residue Count: 1,064 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PPK2 domain-containing protein	A, B, C, D	266	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_0132 EC: 2.7.4.1
UniProt
Find proteins for Q9RY20 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RY20  Go to UniProtKB:  Q9RY20

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth A], F [auth A], H [auth B], L [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth B], I [auth C], J [auth C], K [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 0.246 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.925	α = 90
b = 78.605	β = 109.207
c = 111.451	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
PHASER	phasing
STARANISO	data scaling
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-07 
Deposition Author(s): Silva, S.T.N., Romao, C.

---

Funding Organization	Location	Grant Number
Fundacao para a Ciencia e a Tecnologia	Portugal	--

Revision History  

• Version 1.0: 2021-04-07
  Type: Initial release
  
• Version 1.1: 2021-12-08
  Changes: Database references, Derived calculations
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description