4IJI | pdb_00004iji

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), 0.203 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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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 
  • Modeled Residue Count: 1,598 
  • Deposited Residue Count: 1,712 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione S-transferase-like protein YibF
A, B, C, D, E
A, B, C, D, E, F, G, H
214Pseudomonas protegens Pf-5Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4K4R5
Sequence Annotations
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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]
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
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
A, B, C, D, E, F, G, H
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), 0.203 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.176 (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

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

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