2Z1Y | pdb_00002z1y

Crystal structure of LysN, alpha-aminoadipate aminotransferase (complexed with N-(5'-phosphopyridoxyl)-L-leucine), from Thermus thermophilus HB27

• PDB DOI: https://doi.org/10.2210/pdb2Z1Y/pdb

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


• Deposited: 2007-05-16 Released: 2008-06-03 
• Deposition Author(s): Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.194 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Mechanism of broad substrate specificity of alpha-aminoadipate aminotransferase from Thermus thermophilus

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 (software)

Macromolecule Content 

• Total Structure Weight: 88.56 kDa 
• Atom Count: 6,946 
• Modeled Residue Count: 788 
• Deposited Residue Count: 794 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-aminoadipate transaminase	A, B	397	Thermus thermophilus HB27	Mutation(s): 0  Gene Names: lysN, TT_C0043 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	D [auth A], F [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
LEU	C [auth A], E [auth B]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.194 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.107	α = 90
b = 62.229	β = 116.34
c = 107.439	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Tomita, T., Miyazaki, T., Miyagawa, T., Fushinobu, S., Kuzuyama, T., Nishiyama, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.0: 2025-01-29
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary