2ODK | pdb_00002odk

Putative prevent-host-death protein from Nitrosomonas europaea

• PDB DOI: https://doi.org/10.2210/pdb2ODK/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-22 Released: 2007-01-23 
• Deposition Author(s): Osipiuk, J., Skarina, T., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.154 (Depositor), 0.153 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.132 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Literature

Crsytal structure of putative prevent-host-death protein from Nitrosomonas europaea.

Osipiuk, J., Skarina, T., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A.

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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.79 kDa 
• Atom Count: 2,131 
• Modeled Residue Count: 204 
• Deposited Residue Count: 356 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein	A, B, C, D	89	Nitrosomonas europaea	Mutation(s): 2  Gene Names: NE2111
UniProt
Find proteins for Q82T22 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82T22  Go to UniProtKB:  Q82T22

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth B], F [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-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: 1.40 Å
• R-Value Free:  0.154 (Depositor), 0.153 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.132 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.146	α = 90
b = 78.873	β = 115.96
c = 54.987	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-23 
Deposition Author(s): Osipiuk, J., Skarina, T., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary