3NBM | pdb_00003nbm

The lactose-specific IIB component domain structure of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) from Streptococcus pneumoniae.

• PDB DOI: https://doi.org/10.2210/pdb3NBM/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus pneumoniae TIGR4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-06-03 Released: 2010-09-08 
• Deposition Author(s): Cuff, M.E., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.167 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.125 (DCC) 
• R-Value Observed: 
  0.134 (Depositor) 

Literature

Structure of the lactose-specific IIB component domain of the phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) from Streptococcus pneumoniae.

Cuff, M.E., Chhor, G., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.06 kDa 
• Atom Count: 1,010 
• Modeled Residue Count: 104 
• Deposited Residue Count: 108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system, lactose-specific IIBC components	A	108	Streptococcus pneumoniae TIGR4	Mutation(s): 0  Gene Names: lacE-1, SP_0478 EC: 2.7.1.207
UniProt
Find proteins for A0A0H2UNS1 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)) Explore A0A0H2UNS1  Go to UniProtKB:  A0A0H2UNS1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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: 1.30 Å
• R-Value Free:  0.167 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.125 (DCC) 
• R-Value Observed: 0.134 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.372	α = 90
b = 41.372	β = 90
c = 98.527	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: 2010-09-08 
Deposition Author(s): Cuff, M.E., Chhor, G., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary