3E7N | pdb_00003e7n

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

• PDB DOI: https://doi.org/10.2210/pdb3E7N/pdb
• Entry: 3E7N supersedes: 3DSA

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


• Deposited: 2008-08-18 Released: 2008-08-26 
• Deposition Author(s): Nocek, B., Maltseva, N., Gu, M., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

Crystal structure of d-ribose high-affinity transport system from salmonella typhimurium lt2

Nocek, B., Maltseva, N., Gu, M., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.77 kDa 
• Atom Count: 16,381 
• Modelled Residue Count: 2,101 
• Deposited Residue Count: 2,130 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-ribose high-affinity transport system	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	142	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: rbsD, STM3881 EC: 5.4.99.62
UniProt
Find proteins for Q8ZKW0 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q8ZKW0  Go to UniProtKB:  Q8ZKW0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	AA [auth N], BA [auth O], P [auth A], Q [auth B], R [auth C], S [auth D], T [auth E], U [auth F], V [auth G], W [auth H], X [auth J], Y [auth K], Z [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F, G, H, I, J, K, L, M, N, O	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.233 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m33e7n

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 293.042	α = 90
b = 92.726	β = 106.53
c = 93.601	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELX	phasing
Coot	model building
MLPHARE	phasing
CCP4	phasing
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-26 
Deposition Author(s): Nocek, B., Maltseva, N., Gu, M., Joachimiak, A., Anderson, W., Center for Structural Genomics of Infectious Diseases (CSGID)
• This entry supersedes: 3DSA

Revision History  

• Version 1.0: 2008-08-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary