6DZG | pdb_00006dzg

Crystal structure of polyphosphate kinase 2 class I (SMc02148) in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb6DZG/pdb

• Classification: TRANSFERASE
• Organism(s): Sinorhizobium meliloti 1021
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-07-03 Released: 2019-07-10 
• Deposition Author(s): Nocek, B., Joachimiak, A., Ruszkowski, M., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.87 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structural insights into substrate selectivity and activity of bacterial polyphosphate kinases

Nocek, B., Joachimiak, A., Yakunin, A., Ruszkowski, M.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 143.78 kDa 
• Atom Count: 10,227 
• Modeled Residue Count: 1,152 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate:ADP phosphotransferase 1	A, B, C, D	300	Sinorhizobium meliloti 1021	Mutation(s): 0  Gene Names: SMc02148 EC: 2.7.4.1 (PDB Primary Data), 2.7.4 (UniProt)
UniProt
Find proteins for Q92SA6 (Rhizobium meliloti (strain 1021)) Explore Q92SA6  Go to UniProtKB:  Q92SA6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	E [auth A], G [auth B], J [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP (Subject of Investigation/LOI)	L [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
MLT	F [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	D-MALATE C4 H6 O5 BJEPYKJPYRNKOW-UWTATZPHSA-N

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: 1.87 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.976	α = 75.63
b = 70.563	β = 85.96
c = 89.52	γ = 64.72

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Nocek, B., Joachimiak, A., Ruszkowski, M., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-10-30
  Changes: Structure summary