4IJI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 99TClick on this verticalbar to view details

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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutathione S-transferase-like protein YibF
A, B, C, D, E
214Pseudomonas protegens Pf-5Mutation(s): 0 
Gene Names: yibFPFL_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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4K4R5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
99T
Query on 99T

Download Ideal Coordinates CCD File 
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
L-gamma-glutamyl-S-(2-carboxyethyl)-L-cysteinylglycine
C13 H21 N3 O8 S
ILLXYSCGSHMUFK-YUMQZZPRSA-N
BEZ
Query on BEZ

Download Ideal Coordinates CCD File 
N [auth F],
Q [auth H]
BENZOIC ACID
C7 H6 O2
WPYMKLBDIGXBTP-UHFFFAOYSA-N
AKR
Query on AKR

Download Ideal Coordinates CCD File 
O [auth F],
R [auth H]
ACRYLIC ACID
C3 H4 O2
NIXOWILDQLNWCW-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.763α = 90
b = 190.002β = 101.67
c = 83.6γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 99TClick on this verticalbar to view details

Entry History 

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