3M92 | pdb_00003m92

The structure of yciN, an unchracterized protein from Shigella flexneri.

• PDB DOI: https://doi.org/10.2210/pdb3M92/pdb

• Classification: structural genomics, unknown function
• Organism(s): Shigella flexneri 2a str. 2457T
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2010-03-19 Released: 2010-05-19 
• Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

The structure of yciN, an unchracterized protein from Shigella flexneri.

Cuff, M.E., Xu, X., Cui, H., Chin, S., 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 24.56 kDa 
• Atom Count: 1,377 
• Modeled Residue Count: 161 
• Deposited Residue Count: 214 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein yciN	A, B	107	Shigella flexneri 2a str. 2457T	Mutation(s): 0  Gene Names: S1360, SF1275, yciN
UniProt
Find proteins for P0AB64 (Shigella flexneri) Explore P0AB64  Go to UniProtKB:  P0AB64

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-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: 2.05 Å
• R-Value Free:  0.241 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.35	α = 90
b = 56.35	β = 90
c = 132.26	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
SHELXE	model building
SOLVE	phasing
RESOLVE	phasing
ARP/wARP	model building
CCP4	phasing
O	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Cuff, M.E., Xu, X., Cui, H., Chin, S., Savchenko, A., Edwards, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary