6CE1 | pdb_00006ce1

Crystal structure of Peptidyl Arginine Deiminase Type III (PADI3)

• PDB DOI: https://doi.org/10.2210/pdb6CE1/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2018-02-10 Released: 2019-02-13 
• Deposition Author(s): Rechiche, O., Lee, T.V., Lott, J.S.
• Funding Organization(s): New Zealand Wool Industry Research Limited

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography

Rechiche, O., Lee, T.V., Lott, J.S.

(2021) Acta Crystallogr F Struct Biol Commun 77: 334-340

• DOI: https://doi.org/10.1107/S2053230X21009195

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)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 77.53 kDa 
• Atom Count: 4,253 
• Modeled Residue Count: 594 
• Deposited Residue Count: 686 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-arginine deiminase type-3	A	686	Homo sapiens	Mutation(s): 0  Gene Names: PADI3, PAD3, PDI3 EC: 3.5.3.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULW8 (Homo sapiens) Explore Q9ULW8  Go to UniProtKB:  Q9ULW8
PHAROS:  Q9ULW8 GTEx:  ENSG00000142619

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.274 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.023	α = 90
b = 115.023	β = 90
c = 328.487	γ = 120

Software Package:

Software Name	Purpose
phenix.refine	refinement
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-02-13 
Deposition Author(s): Rechiche, O., Lee, T.V., Lott, J.S.

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Funding Organization	Location	Grant Number
New Zealand Wool Industry Research Limited	New Zealand	A18223

Revision History  

• Version 1.0: 2019-02-13
  Type: Initial release
  
• Version 2.0: 2021-05-19
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Source and taxonomy
• Version 2.1: 2021-10-06
  Changes: Database references
• Version 2.2: 2021-10-13
  Changes: Database references
• Version 2.3: 2023-10-04
  Changes: Data collection, Refinement description