4Z04 | pdb_00004z04

Crystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione

• PDB DOI: https://doi.org/10.2210/pdb4Z04/pdb

• Classification: LYASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-03-25 Released: 2015-04-22 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.161 (Depositor), 0.163 (DCC) 
• R-Value Work: 
  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.135 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a probable lactoylglutathione lyase from Brucella melitensis in complex with glutathione

Abendroth, J., Clifton, M.C., Lorimer, D.D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.07 kDa 
• Atom Count: 1,118 
• Modeled Residue Count: 124 
• Deposited Residue Count: 131 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glyoxalase/Bleomycin resistance /Dioxygenase superfamily protein	A	131	Brucella abortus 2308	Mutation(s): 0  Gene Names: BAB1_1899, DK47_1237
UniProt
Find proteins for Q2YLQ3 (Brucella abortus (strain 2308)) Explore Q2YLQ3  Go to UniProtKB:  Q2YLQ3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
MRD	D [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.161 (Depositor), 0.163 (DCC) 
• R-Value Work:  0.134 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.135 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34Z04

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.63	α = 90
b = 39.5	β = 116.29
c = 41.7	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
BALBES	phasing
PHENIX	model building
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-22 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2015-04-22
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description