3LGX | pdb_00003lgx

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

• PDB DOI: https://doi.org/10.2210/pdb3LGX/pdb

• Classification: ATP binding protein
• Organism(s): Streptococcus pyogenes M1 GAS
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-21 Released: 2010-03-02 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.211 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: experimental

Literature

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 234.6 kDa 
• Atom Count: 16,060 
• Modeled Residue Count: 2,031 
• Deposited Residue Count: 2,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--poly(phosphoribitol) ligase subunit 1	A, B, C, D	521	Streptococcus pyogenes M1 GAS	Mutation(s): 0  Gene Names: dltA, M5005_Spy1073, SPy_1312 EC: 6.1.1.13 (PDB Primary Data), 6.2.1.54 (UniProt)
UniProt
Find proteins for Q99ZA6 (Streptococcus pyogenes serotype M1) Explore Q99ZA6  Go to UniProtKB:  Q99ZA6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth A], F [auth B], G [auth C], H [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.276 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.211 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.41	α = 90
b = 174.41	β = 90
c = 176.065	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description