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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.185 (Depositor), 0.183 (DCC)
R-Value Work:
0.179 (Depositor), 0.177 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4F6P

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
Modeled Residue Count: 261
Deposited Residue Count: 350
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	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] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.185 (Depositor), 0.183 (DCC)
R-Value Work: 0.179 (Depositor), 0.177 (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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.