1WVB | pdb_00001wvb

Crystal structure of human arginase I: the mutant E256Q

• PDB DOI: https://doi.org/10.2210/pdb1WVB/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-12-14 Released: 2005-09-06 
• Deposition Author(s): Di Costanzo, L., Guadalupe, S., Mora, A., Centeno, F., Christianson, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.217 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human arginase I: the mutant E256Q

Di Costanzo, L., Guadalupe, S., Mora, A., Centeno, F., 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.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.2 kDa 
• Atom Count: 4,805 
• Modeled Residue Count: 618 
• 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): 1  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
S2C	E [auth A], H [auth B]	S-2-(BORONOETHYL)-L-CYSTEINE C5 H13 B N O5 S XLVRIIJULVQAMP-BYPYZUCNSA-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: 2.30 Å
• R-Value Free:  0.217 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.272	α = 90
b = 90.272	β = 90
c = 69.305	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALA	data scaling
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-06 
Deposition Author(s): Di Costanzo, L., Guadalupe, S., Mora, A., Centeno, F., Christianson, D.W.

Revision History  

• Version 1.0: 2005-09-06
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-07-16
  Changes: Structure summary
• Version 1.4: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.5: 2023-10-25
  Changes: Data collection, Refinement description