2O8R

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

• PDB DOI: https://doi.org/10.2210/pdb2O8R/pdb

• Classification: TRANSFERASE
• Organism(s): Porphyromonas gingivalis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-12 Released: 2006-12-19 
• Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

Crystal Structure of Polyphosphate Kinase from Porphyromonas Gingivalis

Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.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)

Macromolecule Content

• Total Structure Weight: 167.18 kDa 
• Atom Count: 10,452 
• Modelled Residue Count: 1,253 
• Deposited Residue Count: 1,410 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyphosphate kinase	A, B	705	Porphyromonas gingivalis	Mutation(s): 21  Gene Names: ppk EC: 2.7.4.1
UniProt
Find proteins for Q7MTR1 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83)) Explore Q7MTR1  Go to UniProtKB:  Q7MTR1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	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:  0.255 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.33	α = 90
b = 99.33	β = 90
c = 335.061	γ = 120

Software Package:

Software Name	Purpose
SHELX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-19 
Deposition Author(s): Patskovsky, Y., Toro, R., Sauder, J.M., Dickey, M., Adams, J.M., Ozyurt, S., Wasserman, S.R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2006-12-19
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-11-14
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2021-10-20
  Changes: Database references
• Version 1.6: 2023-12-27
  Changes: Data collection, Refinement description
• Version 1.7: 2024-11-13
  Changes: Structure summary