4YYS

Ficin B crystal form II

PDB DOI: https://doi.org/10.2210/pdb4YYS/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: 1.35 Å
R-Value Free: 0.173
R-Value Work: 0.158
R-Value Observed: 0.159

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 48.56 kDa
Atom Count: 3,918
Modelled Residue Count: 441
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ficin isoform B	A, B	221	Ficus carica	Mutation(s): 0 EC: 3.4.22.3
UniProt
Find proteins for A0A182DW08 (Ficus carica) Explore A0A182DW08 Go to UniProtKB: A0A182DW08
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A182DW08
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.173
R-Value Work: 0.158
R-Value Observed: 0.159
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.055	α = 90
b = 66.961	β = 97
c = 91.266	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Baeyens-Volant, D.

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.