2PHA | pdb_00002pha

Crystal structure of native, unliganded human arginase at 1.90 resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.244 (Depositor) 
  • R-Value Work: 
    0.198 (Depositor), 0.197 (DCC) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of human arginase I complexed with thiosemicarbazide reveals an unusual thiocarbonyl mu-sulfide ligand in the binuclear manganese cluster.

Di Costanzo, L., Pique, M.E., Christianson, D.W.

(2007) J Am Chem Soc 129: 6388-6389

  • DOI: https://doi.org/10.1021/ja071567j
  • Primary Citation Related Structures: 
    2PHA, 2PHO, 2ZAV

  • PubMed Abstract: 

    The crystal structure of the human arginase I-thiosemicarbazide complex reveals an unusual thiocarbonyl μ-sulfide ligand in the binuclear manganese cluster. The C=S moiety of thiosemicarbazide bridges Mn 2+ A and Mn 2+ B with coordination distances of 2.6 Å and 2.4 Å, respectively. Otherwise, the binding of thiosemicarbazide to human arginase I does not cause any significant structural changes in the active site. The crystal structure of the unliganded enzyme reveals a hydrogen bonded water molecule that could support proton transfer between a μ-water molecule and H141 to regenerate the nucleophilic μ-hydroxide ion in the final step of catalysis.

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

Macromolecule Content 

  • Total Structure Weight: 69.78 kDa 
  • Atom Count: 5,032 
  • Modeled Residue Count: 628 
  • Deposited Residue Count: 644 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase-1
A, B
322Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.244 (Depositor) 
  • R-Value Work:  0.198 (Depositor), 0.197 (DCC) 
Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.77α = 90
b = 90.77β = 90
c = 69.74γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2007-12-17
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description