4TKZ | pdb_00004tkz

Crystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae

• PDB DOI: https://doi.org/10.2210/pdb4TKZ/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus agalactiae NEM316
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-28 Released: 2014-08-20 
• Deposition Author(s): Nakamichi, Y., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.
• Funding Organization(s): Grants-in-Aid for Scientific Research for Japan Society for the Promotion of Science, Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology, Research Fellowships from the Japan Society for the Promotion of Science for Young Scientists

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae

Nakamichi, Y., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

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)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.04 kDa 
• Atom Count: 6,369 
• Modeled Residue Count: 780 
• Deposited Residue Count: 912 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein gbs1890	A, B, C, D, E, F	152	Streptococcus agalactiae NEM316	Mutation(s): 0  Gene Names: gbs1890 EC: 2.7.1.69
UniProt
Find proteins for Q8E371 (Streptococcus agalactiae serotype III (strain NEM316)) Explore Q8E371  Go to UniProtKB:  Q8E371

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth D], M [auth D], N [auth D], O [auth D], P [auth E], Q [auth E]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.242 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.293	α = 91.14
b = 53.8	β = 90.02
c = 94.887	γ = 60.97

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Nakamichi, Y., Maruyama, Y., Oiki, S., Mikami, B., Murata, K., Hashimoto, W.

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Funding Organization	Location	Grant Number
Grants-in-Aid for Scientific Research for Japan Society for the Promotion of Science	Japan	--
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology	Japan	--
Research Fellowships from the Japan Society for the Promotion of Science for Young Scientists	Japan	--

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Data collection, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description