3OGH | pdb_00003ogh

Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins

• PDB DOI: https://doi.org/10.2210/pdb3OGH/pdb

• Classification: Structural Genomics, Unknown function
• Organism(s): Escherichia coli O6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-08-16 Released: 2010-09-15 
• Deposition Author(s): Nocek, B., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Literature

Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins

Nocek, B., Bigelow, L., Bearden, J., Joachimiak, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.43 kDa 
• Atom Count: 2,576 
• Modeled Residue Count: 296 
• Deposited Residue Count: 342 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein yciE	A [auth B], B [auth A]	171	Escherichia coli O6	Mutation(s): 0  Gene Names: yciE, c1723
UniProt
Find proteins for A0A0H2V857 (Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)) Explore A0A0H2V857  Go to UniProtKB:  A0A0H2V857

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	D [auth B], G [auth A]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
CL	E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	C [auth B], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.213 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.166 (Depositor), 0.165 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.148	α = 90
b = 90.295	β = 103.51
c = 58.132	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	phasing
SHELX	model building
ARP/wARP	model building
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Nocek, B., Bigelow, L., Bearden, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary