4I97 | pdb_00004i97

The crystal structure of glutathione S-transferase SnigGSTD1A from Scaptomyza nigrita in complex with glutathione

PDB DOI: https://doi.org/10.2210/pdb4I97/pdb

Classification: TRANSFERASE
Organism(s): Scaptomyza nigrita
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-04 Released: 2013-12-04
Deposition Author(s): Hailey, A.L., Montfort, W.R., Weichsel, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.273 (Depositor), 0.262 (DCC)
R-Value Work:
0.219 (Depositor)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Evolution of herbivory by adaption in an ancient detoxification pathway

Gloss, A.D., Vassao, D.G., Schramm, K., Reichelt, M., Hailey, A.L., Rast, T.J., Weichsel, A., Gershenzon, J., Montfort, W.R., Whiteman, N.K.

To be published.

Macromolecule Content

Total Structure Weight: 47.98 kDa
Atom Count: 3,574
Modeled Residue Count: 414
Deposited Residue Count: 416
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DELTA CLASS 1 GLUTATHIONE S-TRANSFERASE	A, B	208	Scaptomyza nigrita	Mutation(s): 0 Gene Names: GstD1A
UniProt
Find proteins for R4S8C5 (Scaptomyza nigrita) Explore R4S8C5 Go to UniProtKB: R4S8C5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	R4S8C5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	C [auth A], D [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.273 (Depositor), 0.262 (DCC)
R-Value Work: 0.219 (Depositor)
R-Value Observed: 0.222 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.29	α = 90
b = 63.29	β = 90
c = 221.41	γ = 90

Software Package:

Software Name	Purpose
MrBUMP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-12-04
Type: Initial release
Version 1.1: 2023-09-20
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.