3DJ8 | pdb_00003dj8

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I

• PDB DOI: https://doi.org/10.2210/pdb3DJ8/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-22 Released: 2008-07-08 
• Deposition Author(s): Di Costanzo, L., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 
  0.193 (Depositor), 0.154 (DCC) 
• R-Value Work: 
  0.152 (Depositor), 0.154 (DCC) 

Starting Model: experimental

Literature

Synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid and structure of its metal-bridging complex with human arginase I

Zakharian, T.Y., Di Costanzo, L., Christianson, D.W.

(2008) Org Biomol Chem 6: 3240-3243

• PubMed: 18802628 
• DOI: https://doi.org/10.1039/b811797g
• Primary Citation Related Structures: 
  3DJ8


• PubMed Abstract: 
  

  The synthesis of (2S)-2-amino-7,8-epoxyoctanoic acid is reported along with the X-ray crystal structure of its complex with human arginase I, revealing unique coordination interactions with two manganese ions in the enzyme active site.

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Organizational Affiliation: 
• Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 70.13 kDa 
• Atom Count: 5,122 
• Modeled Residue Count: 626 
• Deposited Residue Count: 644 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase-1	A, B	322	Homo sapiens	Mutation(s): 0  EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens) Explore P05089  Go to UniProtKB:  P05089
PHAROS:  P05089 GTEx:  ENSG00000118520

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EXY	E [auth A], H [auth B]	6-[(2R)-oxiran-2-yl]-L-norleucine C8 H15 N O3 VESDHWISIJZIDY-RQJHMYQMSA-N
MN	C [auth A], D [auth A], F [auth B], G [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free:  0.193 (Depositor), 0.154 (DCC) 
• R-Value Work:  0.152 (Depositor), 0.154 (DCC) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.623	α = 90
b = 90.623	β = 90
c = 69.56	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-08 
Deposition Author(s): Di Costanzo, L., Christianson, D.W.

Revision History  

• Version 1.0: 2008-07-08
  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