3G12 | pdb_00003g12

Crystal structure of a putative lactoylglutathione lyase from Bdellovibrio bacteriovorus

• PDB DOI: https://doi.org/10.2210/pdb3G12/pdb

• Classification: LYASE
• Organism(s): Bdellovibrio bacteriovorus HD100
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-29 Released: 2009-02-10 
• Deposition Author(s): Patskovsky, Y., Madegowda, M., Gilmore, M., Chang, S., Maletic, M., Smith, D., Sauder, J.M., Burley, S.K., Swaminathan, S., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free: 
  0.275 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Literature

Crystal structure of a putative lactoylglutathione lyase from Bdellovibrio bacteriovorus

Patskovsky, Y., Madegowda, M., Gilmore, M., Chang, S., Maletic, M., Smith, D., Sauder, J.M., Burley, S.K., Swaminathan, S., Almo, S.C.

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: 28.61 kDa 
• Atom Count: 1,775 
• Modeled Residue Count: 223 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative lactoylglutathione lyase	A, B	128	Bdellovibrio bacteriovorus HD100	Mutation(s): 0  Gene Names: Bd2520
UniProt
Find proteins for Q6MK89 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100)) Explore Q6MK89  Go to UniProtKB:  Q6MK89

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.58 Å
• R-Value Free:  0.275 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.276	α = 90
b = 91.276	β = 90
c = 57.711	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SHELXD	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-02-10 
Deposition Author(s): Patskovsky, Y., Madegowda, M., Gilmore, M., Chang, S., Maletic, M., Smith, D., Sauder, J.M., Burley, S.K., Swaminathan, S., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.5: 2024-02-21
  Changes: Data collection, Database references