4HZ2

Crystal structure of glutathione s-transferase xaut_3756 (target efi-507152) from xanthobacter autotrophicus py2

PDB DOI: https://doi.org/10.2210/pdb4HZ2/pdb

Classification: TRANSFERASE
Organism(s): Xanthobacter autotrophicus Py2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-11-14 Released: 2012-11-28
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.199 (Depositor), 0.200 (DCC)
R-Value Work:
0.138 (Depositor), 0.140 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of glutathione s-transferase xaut_3756 from xanthobacter autotrophicus py2

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Zencheck, W.D., Imker, H.J., Al Obaidi, N.F., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 51.56 kDa
Atom Count: 3,817
Modelled Residue Count: 411
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase domain	A, B	230	Xanthobacter autotrophicus Py2	Mutation(s): 0 Gene Names: Xaut_3756
UniProt
Find proteins for A7ILT8 (Xanthobacter autotrophicus (strain ATCC BAA-1158 / Py2)) Explore A7ILT8 Go to UniProtKB: A7ILT8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A7ILT8
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
UNL Query on UNL Download Ideal Coordinates CCD File	E [auth A]	Unknown ligand WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.199 (Depositor), 0.200 (DCC)
R-Value Work: 0.138 (Depositor), 0.140 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.886	α = 90
b = 132.694	β = 90
c = 43.229	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-11-28

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2012-11-28
Type: Initial release
Version 1.1: 2018-01-24
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description