3OXP | pdb_00003oxp

Structure of phosphotransferase enzyme II, A component from Yersinia pestis CO92 at 1.2 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3OXP/pdb

• Classification: TRANSFERASE
• Organism(s): Yersinia pestis CO92
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-09-21 Released: 2010-10-13 
• Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.20 Å
• R-Value Free: 
  0.179 (Depositor), 0.172 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.146 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Literature

Structure of phosphotransferase enzyme II, A component from Yersinia pestis CO92 at 1.2 A resolution

Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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: 32.73 kDa 
• Atom Count: 2,739 
• Modeled Residue Count: 296 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphotransferase enzyme II, A component	A, B	150	Yersinia pestis CO92	Mutation(s): 0  Gene Names: ptsN1, YPO2569, YP_2380, y1618
UniProt
Find proteins for A0A2U2GUN8 (Yersinia pestis) Explore A0A2U2GUN8  Go to UniProtKB:  A0A2U2GUN8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.20 Å
• R-Value Free:  0.179 (Depositor), 0.172 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.146 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33oxp

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.906	α = 90
b = 57.946	β = 90
c = 78.742	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
CCP4	model building
MrBUMP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-13 
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Kudritska, M., Edwards, A., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2010-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary