3K6C

Crystal structure of protein ne0167 from nitrosomonas europaea

• PDB DOI: https://doi.org/10.2210/pdb3K6C/pdb
• Entry: 3K6C supersedes: 1ZPY

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Nitrosomonas europaea
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-08 Released: 2009-10-27 
• Deposition Author(s): Chang, C., Evdokimova, E., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 

Literature

Crystal Structure of Protein Ne0167 from Nitrosomonas Europaea

Chang, C., Evdokimova, E., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

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

Macromolecule Content

• Total Structure Weight: 114.06 kDa 
• Atom Count: 7,911 
• Modelled Residue Count: 909 
• Deposited Residue Count: 950 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein NE0167	A, B, C, D, E, F, G, H, I, J	95	Nitrosomonas europaea	Mutation(s): 0  Gene Names: NE0167
UniProt
Find proteins for Q82XT5 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298)) Explore Q82XT5  Go to UniProtKB:  Q82XT5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.261 
• R-Value Work: 0.221 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.417	α = 90
b = 134.551	β = 96.24
c = 78.458	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
MLPHARE	phasing
DM	model building
RESOLVE	model building
Coot	model building
ARP/wARP	model building
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
DM	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Chang, C., Evdokimova, E., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• This entry supersedes: 1ZPY

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary