2EGY | pdb_00002egy

Crystal structure of LysN, alpha-aminoadipate aminotransferase (substrate free form), from Thermus thermophilus HB27

• PDB DOI: https://doi.org/10.2210/pdb2EGY/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB27
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-02 Released: 2008-03-04 
• Deposition Author(s): Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free: 
  0.294 (Depositor), 0.212 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of LysN, alpha-aminoadipate aminotransferase, from Thermus thermophilus HB27

Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

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,PQS (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,PQS (software)

Macromolecule Content 

• Total Structure Weight: 176.59 kDa 
• Atom Count: 12,341 
• Modeled Residue Count: 1,573 
• Deposited Residue Count: 1,588 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-aminodipate aminotransferase	A, B, C, D	397	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: lysN EC: 2.6.1.39
UniProt
Find proteins for Q72LL6 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27)) Explore Q72LL6  Go to UniProtKB:  Q72LL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	E [auth A], F [auth B], G [auth C], H [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.67 Å
• R-Value Free:  0.294 (Depositor), 0.212 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.415	α = 90
b = 138.51	β = 100.21
c = 111.745	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description