4MZW | pdb_00004mzw

CRYSTAL STRUCTURE OF NU-CLASS GLUTATHIONE TRANSFERASE YGHU FROM Streptococcus sanguinis SK36, COMPLEX WITH GLUTATHIONE DISULFIDE, TARGET EFI-507286

• PDB DOI: https://doi.org/10.2210/pdb4MZW/pdb

• Classification: TRANSFERASE
• Organism(s): Streptococcus sanguinis SK36
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-30 Released: 2013-10-16 
• Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glutathione S-Transferase Yghu (Target Efi-507286)

Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

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: 64.71 kDa 
• Atom Count: 4,739 
• Modeled Residue Count: 531 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-Transferase	A, B	284	Streptococcus sanguinis SK36	Mutation(s): 0  Gene Names: SSA_1418
UniProt
Find proteins for A3CNR0 (Streptococcus sanguinis (strain SK36)) Explore A3CNR0  Go to UniProtKB:  A3CNR0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDS	C [auth A], D [auth B]	OXIDIZED GLUTATHIONE DISULFIDE C20 H32 N6 O12 S2 YPZRWBKMTBYPTK-BJDJZHNGSA-N
ACT	E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.075	α = 90
b = 88.075	β = 90
c = 163.373	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Patskovsky, Y., Toro, R., Bhosle, R., Hillerich, B., Seidel, R.D., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Imker, H.J., Al Obaidi, N., Stead, M., Love, J., Gerlt, J.A., Armstrong, R.N., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description