4O92 | pdb_00004o92

Crystal structure of a Glutathione S-transferase from Pichia kudriavzevii (Issatchenkia orientalis), target EFI-501747

PDB DOI: https://doi.org/10.2210/pdb4O92/pdb

Classification: TRANSFERASE
Organism(s): Pichia kudriavzevii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-31 Released: 2014-01-15
Deposition Author(s): Kim, J., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Washington, E., Glenn, A.S., Chowdhury, S., Evans, B., Stead, M., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Attonito, J.D., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free:
0.258 (Depositor), 0.256 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of a Glutathione S-transferase from Pichia kudriavzevii (Issatchenkia orientalis), target EFI-501747

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

To be published.

Macromolecule Content

Total Structure Weight: 23.57 kDa
Atom Count: 1,538
Modeled Residue Count: 196
Deposited Residue Count: 206
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	206	Pichia kudriavzevii	Mutation(s): 0 Gene Names: GSTY-1, Q9Y727
UniProt
Find proteins for Q9Y727 (Pichia kudriavzevii) Explore Q9Y727 Go to UniProtKB: Q9Y727
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y727
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]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.51 Å
R-Value Free: 0.258 (Depositor), 0.256 (DCC)
R-Value Work: 0.225 (Depositor), 0.230 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.207	α = 90
b = 48.207	β = 90
c = 187.068	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
AutoSol	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-01-15

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2014-01-15
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary