5Y8X | pdb_00005y8x

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine

• PDB DOI: https://doi.org/10.2210/pdb5Y8X/pdb

• Classification: TRANSFERASE
• Organism(s): Bacillus licheniformis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-08-21 Released: 2018-10-17 
• Deposition Author(s): Kumari, S., Goel, M., Pal, R., Gupta, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Bacillus licheniformis Gamma glutamyl transpeptidase with Azaserine

Goel, M., Kumari, S., Gupta, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 64.63 kDa 
• Atom Count: 4,635 
• Modeled Residue Count: 543 
• Deposited Residue Count: 585 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	A	398	Bacillus licheniformis	Mutation(s): 0  EC: 2.3.2.2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma glutamyl transpeptidase	B	187	Bacillus licheniformis	Mutation(s): 0  EC: 2.3.2.2

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AZS	I [auth B]	O-DIAZOACETYL-L-SERINE C5 H7 N3 O4 MZZGOOYMKKIOOX-VKHMYHEASA-N
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	H [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	C [auth A], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.164	α = 90
b = 60.016	β = 100.42
c = 74.781	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-10-17 
Deposition Author(s): Kumari, S., Goel, M., Pal, R., Gupta, R.

Revision History  

• Version 1.0: 2018-10-17
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description