6LFQ

Crystal structure of Poa1p in apo form

PDB DOI: https://doi.org/10.2210/pdb6LFQ/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-03 Released: 2020-12-09
Deposition Author(s): Chiu, Y.C., Hsu, C.H.
Funding Organization(s): Ministry of Science and Technology (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.255
R-Value Work: 0.160
R-Value Observed: 0.169

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Expanding the Substrate Specificity of Macro Domains toward 3''-Isomer of O-Acetyl-ADP-ribose

Chiu, Y.C., Tseng, M.C., Hsu, C.H.

(2021) ACS Catal 11: 11075-11090

DOI: https://doi.org/10.1021/acscatal.1c01943

Macromolecule Content

Total Structure Weight: 20.34 kDa
Atom Count: 1,394
Modelled Residue Count: 169
Deposited Residue Count: 180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribose 1''-phosphate phosphatase	A	180	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: POA1, YBR022W, YBR0304 EC: 3.1.3.84 (PDB Primary Data), 3.2.2 (PDB Primary Data)
UniProt
Find proteins for P38218 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38218 Go to UniProtKB: P38218
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38218
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL 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]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-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: 2.36 Å
R-Value Free: 0.255
R-Value Work: 0.160
R-Value Observed: 0.169
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.195	α = 90
b = 59.612	β = 90
c = 100.658	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-12-09

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (Taiwan)	Taiwan	108-2628-B-002-013
Ministry of Science and Technology (Taiwan)	Taiwan	108-2113-M-002-011

Revision History (Full details and data files)

Version 1.0: 2020-12-09
Type: Initial release
Version 1.1: 2022-06-22
Changes: Database references
Version 1.2: 2024-05-29
Changes: Data collection

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.