1DTY | pdb_00001dty

CRYSTAL STRUCTURE OF ADENOSYLMETHIONINE-8-AMINO-7-OXONANOATE AMINOTRANSFERASE WITH PYRIDOXAL PHOSPHATE COFACTOR.

• PDB DOI: https://doi.org/10.2210/pdb1DTY/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-13 Released: 2000-02-18 
• Deposition Author(s): Alexeev, D., Sawyer, L., Baxter, R.L., Alexeeva, M.V., Campopiano, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free: 
  0.328 (Depositor) 
• R-Value Work: 
  0.196 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Literature

Crystal structure of adenosylmethionine-8-amino-7-oxonanoate aminotransferase with pyridoxal phosphate cofactor

Alexeev, D., Sawyer, L., Baxter, R.L., Alexeeva, M.V., Campopiano, D.

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: 95.45 kDa 
• Atom Count: 7,006 
• Modeled Residue Count: 858 
• Deposited Residue Count: 858 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE	A, B	429	Escherichia coli	Mutation(s): 0  EC: 2.6.1.62
UniProt
Find proteins for P12995 (Escherichia coli (strain K12)) Explore P12995  Go to UniProtKB:  P12995

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.14 Å
• R-Value Free:  0.328 (Depositor) 
• R-Value Work:  0.196 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.28	α = 90
b = 56.27	β = 96.96
c = 121.93	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-18 
Deposition Author(s): Alexeev, D., Sawyer, L., Baxter, R.L., Alexeeva, M.V., Campopiano, D.

Revision History  

• Version 1.0: 2000-02-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2025-03-26
  Changes: Data collection, Database references, Derived calculations, Structure summary