3R4Q | pdb_00003r4q

Crystal structure of Lactoylglutathione lyase from Agrobacterium tumefaciens

• PDB DOI: https://doi.org/10.2210/pdb3R4Q/pdb

• Classification: LYASE
• Organism(s): Agrobacterium fabrum str. C58
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-03-17 Released: 2011-04-06 
• Deposition Author(s): Agarwal, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free: 
  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystal structure of Lactoylglutathione lyase from Agrobacterium tumefaciens

Agarwal, R., Almo, S.C., Swaminathan, S.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 92.69 kDa 
• Atom Count: 5,510 
• Modeled Residue Count: 673 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoylglutathione lyase	A, B, C, D, E	160	Agrobacterium fabrum str. C58	Mutation(s): 0  Gene Names: AGR_C_4259, Atu2344
UniProt
Find proteins for Q7CXA0 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore Q7CXA0  Go to UniProtKB:  Q7CXA0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	G [auth A], H [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
CO	F [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.51 Å
• R-Value Free:  0.296 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.53	α = 90
b = 202.522	β = 90
c = 50.907	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
SHELXD	phasing
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-06 
Deposition Author(s): Agarwal, R., Almo, S.C., Swaminathan, S., New York Structural Genomics Research Consortium (NYSGRC)

Revision History  

• Version 1.0: 2011-04-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations