3L8C | pdb_00003l8c

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

• PDB DOI: https://doi.org/10.2210/pdb3L8C/pdb

• Classification: LIGASE
• Organism(s): Streptococcus pyogenes serotype M6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-12-30 Released: 2010-01-19 
• 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: 2.41 Å
• R-Value Free: 
  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

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

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 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 116.29 kDa 
• Atom Count: 7,946 
• Modeled Residue Count: 1,009 
• Deposited Residue Count: 1,042 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--poly(phosphoribitol) ligase subunit 1	A, B	521	Streptococcus pyogenes serotype M6	Mutation(s): 0  Gene Names: dltA, M6_Spy1043 EC: 6.1.1.13 (PDB Primary Data), 6.2.1.54 (UniProt)
UniProt
Find proteins for Q5XBN5 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XBN5  Go to UniProtKB:  Q5XBN5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free:  0.275 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.024	α = 90
b = 153.736	β = 90
c = 84.794	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
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: 2010-01-19
  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, Structure summary
• Version 1.4: 2024-02-21
  Changes: Data collection, Database references