2YRI | pdb_00002yri

Crystal structure of alanine-pyruvate aminotransferase with 2-methylserine

• PDB DOI: https://doi.org/10.2210/pdb2YRI/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2007-04-02 Released: 2008-04-15 
• Deposition Author(s): Miyahara, I., Matsumura, M., Goto, M., Omi, R., Hirotsu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.191 (Depositor) 

Literature

hypothetical alanine aminotransferase (TTHA0173) from Thermus thermophilus HB8

Miyahara, I., Matsumura, M., Goto, M., Omi, R., Hirotsu, K.

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: 76.38 kDa 
• Atom Count: 6,004 
• Modeled Residue Count: 704 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class V	A, B	353	Thermus thermophilus HB8	Mutation(s): 0  EC: 2.6
UniProt
Find proteins for Q5SLX0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLX0  Go to UniProtKB:  Q5SLX0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MMM	C [auth A]	(S,E)-3-HYDROXY-2-((3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL)METHYLENEAMINO)-2-METHYLPROPANOIC ACID C12 H17 N2 O8 P ASXDVUDIJQGHKR-DRRTZOGYSA-N
PMP	D [auth B]	4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE C8 H13 N2 O5 P ZMJGSOSNSPKHNH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.191 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.299	α = 90
b = 81.299	β = 90
c = 204.082	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
AMoRE	phasing
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Miyahara, I., Matsumura, M., Goto, M., Omi, R., Hirotsu, K., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations