5XLU | pdb_00005xlu

High Resolution Crystal Structure of Bacillus Licheniformis Gamma Glutamyl Transpeptidase with Acivicin

• PDB DOI: https://doi.org/10.2210/pdb5XLU/pdb

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


• Deposited: 2017-05-11 Released: 2018-05-16 
• Deposition Author(s): Kumari, S., Goel, M., Gupta, R., Pal, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

High Resolution Crystal Structure of Bacillus Licheniformis Gamma Glutamyl Transpeptidase with Acivicin

Kumari, S., Goel, M., 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: 64.4 kDa 
• Atom Count: 5,021 
• Modeled Residue Count: 540 
• 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 (PDB Primary Data), 3.4.19.13 (UniProt)
UniProt
Find proteins for Q65KZ6 (Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / CCUG 7422 / NBRC 12200 / NCIMB 9375 / NCTC 10341 / NRRL NRS-1264 / Gibson 46)) Explore Q65KZ6  Go to UniProtKB:  Q65KZ6

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 (PDB Primary Data), 3.4.19.13 (UniProt)
UniProt
Find proteins for A9YTT0 (Bacillus licheniformis) Explore A9YTT0  Go to UniProtKB:  A9YTT0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AVN	D [auth B]	(2S)-AMINO[(5S)-3-CHLORO-4,5-DIHYDROISOXAZOL-5-YL]ACETIC ACID C5 H7 Cl N2 O3 QAWIHIJWNYOLBE-OKKQSCSOSA-N
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.205 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.005	α = 90
b = 85.732	β = 90
c = 124.664	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data processing
PHASER	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Kumari, S., Goel, M., Gupta, R., Pal, R.

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-09-19
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-23
  Changes: Structure summary