7DW4 | pdb_00007dw4

Crystal structure of a glutathione S-transferase mutant SbGSTU6(I55T) from Salix babylonica in complex with glutathione

PDB DOI: https://doi.org/10.2210/pdb7DW4/pdb

Classification: TRANSFERASE
Organism(s): Salix babylonica
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-01-15 Released: 2021-08-04
Deposition Author(s): Zhuge, X.L., Yang, H.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.227 (Depositor), 0.230 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a glutathione S-transferase mutant SbGSTU6(I55T) from Salix babylonica in complex with glutathione

Zhuge, X.L., Yang, H.L.

To be published.

Macromolecule Content

Total Structure Weight: 26.65 kDa
Atom Count: 1,912
Modeled Residue Count: 220
Deposited Residue Count: 235
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A	235	Salix babylonica	Mutation(s): 1 Gene Names: GSTU6 EC: 2.5.1.18
UniProt
Find proteins for A0A4Y5R032 (Salix babylonica) Explore A0A4Y5R032 Go to UniProtKB: A0A4Y5R032
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Y5R032
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH (Subject of Investigation/LOI) Query on GSH 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]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free: 0.227 (Depositor), 0.230 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.379	α = 90
b = 104.379	β = 90
c = 53.126	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-08-04

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	NSFC 32071486

Revision History (Full details and data files)

Version 1.0: 2021-08-04
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, 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.