4YYV | pdb_00004yyv

Ficin isoform C crystal form II

• PDB DOI: https://doi.org/10.2210/pdb4YYV/pdb

• Classification: HYDROLASE
• Organism(s): Ficus carica
• Mutation(s): No 


• Deposited: 2015-03-24 Released: 2016-04-13 
• Deposition Author(s): Azarkan, M., Baeyens-Volant, D., Loris, R.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of four variants of the protease Ficin from the common fig

Baldacci-Cresp, F., Rodriguez Buitrago, J.A., M'Rabet, N., Loris, R., Baucher, M., Baeyens-Volant, D., Azarkan, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 25.02 kDa 
• Atom Count: 1,890 
• Modeled Residue Count: 221 
• Deposited Residue Count: 222 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ficin isoform C	A	222	Ficus carica	Mutation(s): 0  EC: 3.4.22.3
UniProt
Find proteins for A0A182DW09 (Ficus carica) Explore A0A182DW09  Go to UniProtKB:  A0A182DW09

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
16P	G [auth A]	3,6,9,12,15,18-HEXAOXAICOSANE C14 H30 O6 IXFAFGFZFQHRLB-UHFFFAOYSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.244 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.471	α = 90
b = 52.471	β = 90
c = 157.229	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Azarkan, M., Baeyens-Volant, D., Loris, R.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description