4F6P | pdb_00004f6p

Crystal structure of the yeast metacaspase Yca1 C276A mutant

• PDB DOI: https://doi.org/10.2210/pdb4F6P/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-05-15 Released: 2013-03-27 
• Deposition Author(s): Wong, A.H., Yan, C.Y., Shi, Y.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the metacaspase Yca1

Wong, A.H., Yan, C.Y., Shi, Y.G.

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: 38.78 kDa 
• Atom Count: 2,313 
• Modeled Residue Count: 261 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metacaspase-1	A	350	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: MCA1, YCA1, YOR197W EC: 3.4.22
UniProt
Find proteins for Q08601 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08601  Go to UniProtKB:  Q08601

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DFH	B [auth A]	1,1-diphenylethanol C14 H14 O GIMDPFBLSKQRNP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.4	α = 90
b = 114.4	β = 90
c = 61.679	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Wong, A.H., Yan, C.Y., Shi, Y.G.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description