3MJL | pdb_00003mjl

Crystal structure of human arginase I in complex with 2-aminoimidazole. Resolution 1.90 A.

• PDB DOI: https://doi.org/10.2210/pdb3MJL/pdb

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


• Deposited: 2010-04-13 Released: 2010-05-05 
• Deposition Author(s): Di Costanzo, L., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.176 (Depositor), 0.161 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.132 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human arginase I in complex with 2-aminoimidazole. Resolution 1.90 A.

Ilies, M., Di Costanzo, L., North, M.L., Scott, J.A., Christianson, D.W.

To be published.

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: 69.95 kDa 
• Atom Count: 5,032 
• Modeled Residue Count: 627 
• 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  Gene Names: ARG1 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
2AI	E [auth A], H [auth B]	1H-imidazol-2-amine C3 H5 N3 DEPDDPLQZYCHOH-UHFFFAOYSA-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: 1.90 Å
• R-Value Free:  0.176 (Depositor), 0.161 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.132 (DCC) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.68	α = 90
b = 90.68	β = 90
c = 69.82	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Di Costanzo, L., Christianson, D.W.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2018-05-30
  Changes: Data collection, Derived calculations
• Version 1.4: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.5: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description