3LN6 | pdb_00003ln6

Crystal structure of a bifunctional glutathione synthetase from Streptococcus agalactiae

PDB DOI: https://doi.org/10.2210/pdb3LN6/pdb

Classification: LIGASE
Organism(s): Streptococcus agalactiae serogroup V
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-02 Released: 2011-04-13
Deposition Author(s): Stout, J., Vergauwen, B., Savvides, S.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free:
0.286 (Depositor), 0.288 (DCC)
R-Value Work:
0.253 (Depositor), 0.253 (DCC)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3LN6

This is version 1.2 of the entry. See complete history.

Literature

Structures of two bifunctional gamma-Glutamate-cysteine Ligase/Glutathione synthetases (GshF) reveal a novel hybrid ATP-grasp fold

Stout, J., De Vos, D., Vergauwen, B., Savvides, S.N.

To be published.

Macromolecule Content

Total Structure Weight: 85.79 kDa
Atom Count: 5,533
Modeled Residue Count: 743
Deposited Residue Count: 750
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione biosynthesis bifunctional protein gshAB	A	750	Streptococcus agalactiae serogroup V	Mutation(s): 0 Gene Names: gshAB, gshF, SAG1821 EC: 6.3.2.2 (PDB Primary Data), 6.3.2.3 (PDB Primary Data)
UniProt
Find proteins for Q8DXM9 (Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R)) Explore Q8DXM9 Go to UniProtKB: Q8DXM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DXM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.95 Å
R-Value Free: 0.286 (Depositor), 0.288 (DCC)
R-Value Work: 0.253 (Depositor), 0.253 (DCC)

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.02	α = 90
b = 143.02	β = 90
c = 211.23	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data processing
SOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-04-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-13
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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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.