2OMO | pdb_00002omo

Putative antibiotic biosynthesis monooxygenase from Nitrosomonas europaea

• PDB DOI: https://doi.org/10.2210/pdb2OMO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-22 Released: 2007-01-30 
• Deposition Author(s): Osipiuk, J., Evdokimova, E., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 
  0.228 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.190 (Depositor) 
• R-Value Observed: 
  0.191 (Depositor) 

Literature

X-ray structure of putative antibiotic biosynthesis monooxygenase from Nitrosomonas europaea.

Osipiuk, J., Evdokimova, E., 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 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.15 kDa 
• Atom Count: 7,428 
• Modeled Residue Count: 807 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF176	A, B, C, D, E, F, G, H	124	Nitrosomonas europaea	Mutation(s): 4  Gene Names: NE0621
UniProt
Find proteins for Q82WP3 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82WP3  Go to UniProtKB:  Q82WP3

Small Molecules

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A, B, C, D, E, F, G, H	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free:  0.228 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.190 (Depositor) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.155	α = 90
b = 99.248	β = 90
c = 192.672	γ = 90

Software Package:

Software Name	Purpose
SHELXD	phasing
MLPHARE	phasing
DM	model building
SOLVE	phasing
RESOLVE	model building
HKL-2000	data scaling
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing
RESOLVE	phasing
HKL-3000	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-01-30 
Deposition Author(s): Osipiuk, J., Evdokimova, E., Kagan, O., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-11-13
  Changes: Structure summary