3MFX

Crystal Structure of the sensory box domain of the sensory-box/GGDEF protein SO_1695 from Shewanella oneidensis, Northeast Structural Genomics Consortium Target SoR288B

• PDB DOI: https://doi.org/10.2210/pdb3MFX/pdb

• Classification: TRANSCRIPTION
• Organism(s): Shewanella oneidensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-04 Released: 2010-04-14 
• Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 

Literature

Northeast Structural Genomics Consortium Target SoR288B

Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

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)

Macromolecule Content

• Total Structure Weight: 44.93 kDa 
• Atom Count: 2,779 
• Modelled Residue Count: 339 
• Deposited Residue Count: 387 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sensory box/GGDEF family protein	A, B, C	129	Shewanella oneidensis	Mutation(s): 0  Gene Names: SO_1695
UniProt
Find proteins for Q8EGB0 (Shewanella oneidensis (strain MR-1)) Explore Q8EGB0  Go to UniProtKB:  Q8EGB0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.252 
• R-Value Work: 0.205 
• R-Value Observed: 0.207 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.171	α = 90
b = 70.171	β = 90
c = 341.762	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-14 
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2010-04-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description