4IJI

Crystal structure of a glutathione transferase family member from Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-glutathione

PDB DOI: https://doi.org/10.2210/pdb4IJI/pdb

Classification: TRANSFERASE
Organism(s): Pseudomonas protegens Pf-5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-12-21 Released: 2013-02-20
Deposition Author(s): Vetting, M.W., Sauder, J.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Burley, S.K., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.169
R-Value Observed: 0.171

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of a glutathione transferase family member from Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-glutathione

Vetting, M.W., Sauder, J.M., Morisco, L.L., Wasserman, S.R., Sojitra, S., Imker, H.J., Burley, S.K., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

To be published.

Macromolecule Content

Total Structure Weight: 197.97 kDa
Atom Count: 15,230
Modelled Residue Count: 1,598
Deposited Residue Count: 1,712
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-like protein YibF	A, B, C, D, E A, B, C, D, E, F, G, H	214	Pseudomonas protegens Pf-5	Mutation(s): 0 Gene Names: yibF, PFL_5710
UniProt
Find proteins for Q4K4R5 (Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)) Explore Q4K4R5 Go to UniProtKB: Q4K4R5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4K4R5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
99T Query on 99T Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth D] SDF format, chain M [auth E] SDF format, chain P [auth G] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth D] MOL2 format, chain M [auth E] MOL2 format, chain P [auth G] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain L [auth D] mmCIF format, chain M [auth E] mmCIF format, chain P [auth G]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], P [auth G]	L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine C₁₃ H₂₁ N₃ O₈ S ILLXYSCGSHMUFK-YUMQZZPRSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain P [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain P [auth G]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain Q [auth H] MOL2 format, chain N [auth F] MOL2 format, chain Q [auth H] mmCIF format, chain N [auth F] mmCIF format, chain Q [auth H]	N [auth F], Q [auth H]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain N [auth F] Focus chain Q [auth H] Interactions & Density Focus chain N [auth F] Focus chain Q [auth H]
AKR Query on AKR Download Ideal Coordinates CCD File SDF format, chain O [auth F] SDF format, chain R [auth H] MOL2 format, chain O [auth F] MOL2 format, chain R [auth H] mmCIF format, chain O [auth F] mmCIF format, chain R [auth H]	O [auth F], R [auth H]	ACRYLIC ACID C₃ H₄ O₂ NIXOWILDQLNWCW-UHFFFAOYSA-N		Interactions Focus chain O [auth F] Focus chain R [auth H] Interactions & Density Focus chain O [auth F] Focus chain R [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.198
R-Value Work: 0.169
R-Value Observed: 0.171
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.763	α = 90
b = 190.002	β = 101.67
c = 83.6	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-20

Deposition Author(s):

Enzyme Function Initiative (EFI)

Revision History (Full details and data files)

Version 1.0: 2013-02-20
Type: Initial release
Version 1.1: 2018-11-21
Changes: Data collection, Structure summary
Version 1.2: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Structure summary

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4IJI

Crystal structure of a glutathione transferase family member from Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-glutathione

Crystal structure of a glutathione transferase family member from Psuedomonas fluorescens Pf-5, target EFI-900011, with bound S-(propanoic acid)-glutathione

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)