4GF0 | pdb_00004gf0

Crystal structure of glutahtione transferase homolog from sulfitobacter, TARGET EFI-501084, with bound glutathione

PDB DOI: https://doi.org/10.2210/pdb4GF0/pdb

Classification: TRANSFERASE
Organism(s): Sulfitobacter sp. NAS-14.1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-08-02 Released: 2012-08-29
Deposition Author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.193 (Depositor), 0.194 (DCC)
R-Value Work:
0.165 (Depositor), 0.168 (DCC)
R-Value Observed:
0.166 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glutahtione transferase homolog from sulfitobacter, TARGET EFI-501084, with bound glutathione

Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Armstrong, R.N., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 47.54 kDa
Atom Count: 3,333
Modeled Residue Count: 394
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A, B	215	Sulfitobacter sp. NAS-14.1	Mutation(s): 0 Gene Names: NAS141_10626

Small Molecules

Ligands 2 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 A] SDF format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth B]	D [auth A], E [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.193 (Depositor), 0.194 (DCC)
R-Value Work: 0.165 (Depositor), 0.168 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.844	α = 90
b = 95.844	β = 90
c = 94.911	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description