3SOY | pdb_00003soy

Nuclear transport factor 2 (NTF2-like) superfamily protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

• PDB DOI: https://doi.org/10.2210/pdb3SOY/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-06-30 Released: 2011-08-10 
• Deposition Author(s): Cuff, M.E., Li, H., Jedrzejczak, R., Brown, R.N., Adkins, J.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Literature

Nuclear transport factor 2 (NTF2-like) superfamily protein from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Cuff, M.E., Li, H., Jedrzejczak, R., Brown, R.N., Adkins, J.N., Joachimiak, A.

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)

Macromolecule Content 

• Total Structure Weight: 16.54 kDa 
• Atom Count: 1,216 
• Modeled Residue Count: 142 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NTF2-like superfamily protein	A	145	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: STM1528
UniProt
Find proteins for Q8ZPH9 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZPH9  Go to UniProtKB:  Q8ZPH9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLI	B [auth A]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	D [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.346	α = 90
b = 79.346	β = 90
c = 107.293	γ = 90

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: 2011-08-10 
Deposition Author(s): Cuff, M.E., Li, H., Jedrzejczak, R., Brown, R.N., Adkins, J.N., Joachimiak, A., Midwest Center for Structural Genomics (MCSG), Program for the Characterization of Secreted Effector Proteins (PCSEP)

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary