3EQX | pdb_00003eqx

CRYSTAL STRUCTURE OF A FIC FAMILY PROTEIN (SO_4266) FROM SHEWANELLA ONEIDENSIS AT 1.6 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb3EQX/pdb
• Entry: 3EQX supersedes: 2QC0

• Classification: DNA BINDING PROTEIN
• Organism(s): Shewanella oneidensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-01 Released: 2008-10-14 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Literature

Crystal structure of the Fic (Filamentation induced by cAMP) family protein SO4266 (gi|24375750) from Shewanella oneidensis MR-1 at 1.6 A resolution.

Das, D., Krishna, S.S., McMullan, D., Miller, M.D., Xu, Q., Abdubek, P., Acosta, C., Astakhova, T., Axelrod, H.L., Burra, P., Carlton, D., Chiu, H.J., Clayton, T., Deller, M.C., Duan, L., Elias, Y., Elsliger, M.A., Ernst, D., Feuerhelm, J., Grzechnik, A., Grzechnik, S.K., Hale, J., Han, G.W., Jaroszewski, L., Jin, K.K., Klock, H.E., Knuth, M.W., Kozbial, P., Kumar, A., Marciano, D., Morse, A.T., Murphy, K.D., Nigoghossian, E., Okach, L., Oommachen, S., Paulsen, J., Reyes, R., Rife, C.L., Sefcovic, N., Tien, H., Trame, C.B., Trout, C.V., van den Bedem, H., Weekes, D., White, A., Hodgson, K.O., Wooley, J., Deacon, A.M., Godzik, A., Lesley, S.A., Wilson, I.A.

(2009) Proteins 75: 264-271

• PubMed: 19127588 
• DOI: https://doi.org/10.1002/prot.22338
• Primary Citation Related Structures: 
  3EQX

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Organizational Affiliation: 
• Joint Center for Structural Genomics, Stanford University, Menlo Park, California, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 85.45 kDa 
• Atom Count: 6,829 
• Modeled Residue Count: 731 
• Deposited Residue Count: 746 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIC DOMAIN CONTAINING TRANSCRIPTIONAL REGULATOR	A, B	373	Shewanella oneidensis	Mutation(s): 0  Gene Names: NP_719793.1, SO_4266 EC: 2.7.7.108
UniProt
Find proteins for Q8E9K5 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1)) Explore Q8E9K5  Go to UniProtKB:  Q8E9K5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	C [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-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: 1.60 Å
• R-Value Free:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33EQX

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.21	α = 90
b = 80.3	β = 90
c = 141	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• This entry supersedes: 2QC0

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations
• Version 1.5: 2024-11-20
  Changes: Data collection, Refinement description, Structure summary