4F6P

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.185
R-Value Work: 0.179
R-Value Observed: 0.179

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of the metacaspase Yca1

Wong, A.H., Yan, C.Y., Shi, Y.G.

To be published.

Macromolecule Content

Total Structure Weight: 38.78 kDa
Atom Count: 2,313
Modelled Residue Count: 261
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

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)) Go to UniProtKB: Q08601
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DFH Query on DFH Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1,1-diphenylethanol C₁₄ H₁₄ O GIMDPFBLSKQRNP-UHFFFAOYSA-N		Interactions Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.185
R-Value Work: 0.179
R-Value Observed: 0.179
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

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