3L8C

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt
Find proteins for Q5XBN5 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XBN5 Go to UniProtKB: Q5XBN5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5XBN5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.275
R-Value Work: 0.217
R-Value Observed: 0.220
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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-01-19

Deposition Author(s):

Ramagopal, U.A.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.