6FMG | pdb_00006fmg

Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb6FMG/pdb

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


• Deposited: 2018-01-31 Released: 2019-03-13 
• Deposition Author(s): Magoch, M., Grudnik, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structure of the Mannose Transporter IIA Domain from Streptococcus pneumoniae

Magoch, M., Grudnik, P., Nogly, P., Dubin, G., Archer, M., Ma, P.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 60.19 kDa 
• Atom Count: 4,662 
• Modeled Residue Count: 560 
• Deposited Residue Count: 560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTS system mannose-specific transporter subunit IIAB	A, B, C, D	140	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: manL_2, ERS020456_01132 EC: 2.7.1.69

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.528	α = 90
b = 138.528	β = 90
c = 69.767	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
SCALA	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-13 
Deposition Author(s): Magoch, M., Grudnik, P.

Revision History  

• Version 1.0: 2019-03-13
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description