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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.275 (Depositor), 0.271 (DCC)
R-Value Work:
0.217 (Depositor), 0.213 (DCC)
R-Value Observed:
0.220 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3L8C

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
Modeled Residue Count: 1,009
Deposited Residue Count: 1,042
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.271 (DCC)
R-Value Work: 0.217 (Depositor), 0.213 (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

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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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.